Snakemake Report

Jobs 1

Input files

/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/indiv_missingness/indiv_missingness.pgen
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test11/ImputationTestDataset_plink/hg19_input.psam
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/separate_indivs/sex_update_indivs.tsv
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/separate_indivs/remove_indivs.tsv

Output files

/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/update_sex_ancestry/update_sex.pgen
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/update_sex_ancestry/update_sex.pvar
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/update_sex_ancestry/update_sex.psam

Code

        singularity exec --bind {params.bind} {params.sif} mkdir -p {params.tdir}
        singularity exec --bind {params.bind} {params.sif} cp {params.infile}* {params.tdir}
        singularity exec --bind {params.bind} {params.sif} cp {params.anc_updated_psam} {params.tdir}/indiv_missingness.psam 
        singularity exec --bind {params.bind} {params.sif} plink2 --threads {threads} --pfile {params.tdir}/indiv_missingness --update-sex {input.update_sex} --remove {input.remove_indiv} --make-pgen 'psam-cols='fid,parents,sex,phenos --out {params.out}

Jobs 1

Input files

/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test11/ImputationTestDataset_plink/hg19_input.pgen
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test11/ImputationTestDataset_plink/hg19_input.pvar
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test11/ImputationTestDataset_plink/hg19_input.psam

Output files

/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/indiv_missingness/indiv_missingness.pgen
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/indiv_missingness/indiv_missingness.pvar
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/indiv_missingness/indiv_missingness.psam

Code

1
2
3

        singularity exec --bind {params.bind} {params.sif} echo {params.infile}
        singularity exec --bind {params.bind} {params.sif} plink2 --threads {threads}             --pfile {params.infile}             --make-pgen 'psam-cols='fid,parents,sex,phenos             --mind {params.mind}             --out {params.out}

Jobs 1

Input files

/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/pca_sex_checks/check_sex_update_remove.tsv
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/pca_sex_checks/ancestry_update_remove.tsv

Output files

/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/separate_indivs/sex_update_indivs.tsv
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/separate_indivs/remove_indivs.tsv
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/separate_indivs/remove_indivs_temp.tsv

Code

        singularity exec --bind {params.bind} {params.sif} grep "UPDATE" {input.sexcheck} | singularity exec --bind {params.bind} {params.sif} awk 'BEGIN{{FS=OFS="	"}}{{print($1,$2,$4)}}' | singularity exec --bind {params.bind} {params.sif} sed 's/SNPSEX/SEX/g' > {output.update_sex}
        singularity exec --bind {params.bind} {params.sif} grep "REMOVE" {input.sexcheck} | singularity exec --bind {params.bind} {params.sif} awk 'BEGIN{{FS=OFS="	"}}{{print($1,$2)}}'> {output.remove_indiv_temp}
        singularity exec --bind {params.bind} {params.sif} grep "REMOVE" {input.anc_check} | singularity exec --bind {params.bind} {params.sif} awk 'BEGIN{{FS=OFS="	"}}{{print($1,$2)}}' >> {output.remove_indiv_temp}
        singularity exec --bind {params.bind} {params.sif} sort -u {output.remove_indiv_temp} > {output.remove_indiv}

Jobs 1

Input files

/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/pca_projection/final_subset_pruned_data_pcs.sscore
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/pca_projection/subset_pruned_1000g_pcs_projected.sscore
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/common_snps/subset_1000g.psam
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test11/ImputationTestDataset_plink/hg19_input.psam
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/check_sex/check_sex.sexcheck.tsv

Output files

/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/pca_sex_checks/check_sex_update_remove.tsv
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/pca_sex_checks/ancestry_update_remove.tsv
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/pca_sex_checks/Ancestry_PCAs.png

Code

        singularity exec --bind {params.bind} {params.sif} echo {params.outdir} > {params.variables}
        singularity exec --bind {params.bind} {params.sif} echo {input.projected_scores} >> {params.variables}
        singularity exec --bind {params.bind} {params.sif} echo {input.projected_1000g_scores} >> {params.variables}
        singularity exec --bind {params.bind} {params.sif} echo {input.fam_1000g} >> {params.variables}
        singularity exec --bind {params.bind} {params.sif} echo {input.psam} >> {params.variables}
        singularity exec --bind {params.bind} {params.sif} echo {input.sexcheck} >> {params.variables}
        singularity exec --bind {params.bind} {params.sif} Rscript {params.script} {params.variables}

Jobs 1

Input files

/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/common_snps/final_subset_pruned_data.pgen
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/common_snps/final_subset_pruned_data.pvar
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/common_snps/final_subset_pruned_data.psam
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/pca_projection/subset_pruned_1000g_pcs.acount
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/pca_projection/subset_pruned_1000g_pcs.eigenvec.allele

Output files

/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/pca_projection/final_subset_pruned_data_pcs.sscore
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/pca_projection/subset_pruned_1000g_pcs_projected.sscore

Code

        export OMP_NUM_THREADS={threads}
        singularity exec --bind {params.bind} {params.sif} plink2 --threads {threads} --pfile {params.infile}             --read-freq {input.frq}             --score {input.scores} 2 5 header-read no-mean-imputation                     variance-standardize             --score-col-nums 6-15             --out {params.out}
        singularity exec --bind {params.bind} {params.sif} plink2 --threads {threads} --pfile {params.infile_1000g}             --read-freq {input.frq}             --score {input.scores} 2 5 header-read no-mean-imputation                     variance-standardize             --score-col-nums 6-15             --out {params.out_1000g}

Jobs 1

Input files

/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/common_snps/subset_pruned_data.pgen
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/common_snps/subset_pruned_data.pvar
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/common_snps/subset_pruned_data.psam

Output files

/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/common_snps/final_subset_pruned_data.pgen
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/common_snps/final_subset_pruned_data.pvar
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/common_snps/final_subset_pruned_data.psam

Code

1 2	`singularity exec --bind {params.bind} {params.sif} plink2 --rm-dup 'force-first' -threads {threads} --pfile {params.infile} --make-pgen 'psam-cols='fid,parents,sex,phenos --out {params.out}`

Jobs 1

Input files

/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/common_snps/subset_1000g.pgen
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/common_snps/subset_1000g.pvar
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/common_snps/subset_1000g.psam
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/common_snps/subset_data.pvar
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/common_snps/subset_data.pgen
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/common_snps/subset_data.psam

Output files

/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/common_snps/subset_pruned_1000g.prune.out
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/common_snps/subset_data.prune.out
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/common_snps/subset_pruned_1000g.pgen
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/common_snps/subset_pruned_1000g.pvar
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/common_snps/subset_pruned_1000g.psam
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/common_snps/subset_pruned_data.pgen
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/common_snps/subset_pruned_data.pvar
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/common_snps/subset_pruned_data_temp.pvar
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/common_snps/subset_pruned_data_original.pvar
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/common_snps/subset_pruned_data.psam
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/common_snps/subset_pruned_data_1000g_key.txt
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/common_snps/SNPs2keep.txt

Code

        singularity exec --bind {params.bind} {params.sif} plink2 --threads {threads} --pfile {params.infile_1000g}             --indep-pairwise 50 5 0.5             --out {params.out_1000g}
        singularity exec --bind {params.bind} {params.sif} plink2 --threads {threads} --pfile {params.infile_1000g} --extract {output.prune_out_1000g} --make-pgen --out {params.out_1000g}
        if [[ $(grep "##" {input.bim} | wc -l) > 0 ]]
        then
            singularity exec --bind {params.bind} {params.sif} grep "##" {input.bim} > {output.data_1000g_key}
        fi
        singularity exec --bind {params.bind} {params.sif} awk -F"\t" 'BEGIN{{OFS=FS = "\t"}} NR==FNR{{a[$1 FS $2 FS $4 FS $5] = $0; next}} {{ind = $1 FS $2 FS $4 FS $5}} ind in a {{print a[ind], $3}}' {output.bim_1000g} {input.bim} | singularity exec --bind {params.bind} {params.sif} grep -v "##" >> {output.data_1000g_key}
        singularity exec --bind {params.bind} {params.sif} grep -v "##" {output.data_1000g_key} | singularity exec --bind {params.bind} {params.sif} awk 'BEGIN{{FS=OFS="	"}}{{print $NF}}' > {output.prune_out}
        singularity exec --bind {params.bind} {params.sif} plink2 --threads {threads} --pfile {params.infile} --extract {output.prune_out} --make-pgen 'psam-cols='fid,parents,sex,phenos --out {params.out}
        singularity exec --bind {params.bind} {params.sif} cp {output.bim} {output.bim_old}
        singularity exec --bind {params.bind} {params.sif} grep -v "#" {output.bim_old} | singularity exec --bind {params.bind} {params.sif} awk 'BEGIN{{FS=OFS="	"}}{{print($3)}}' > {output.SNPs2keep}
        singularity exec --bind {params.bind} {params.sif} grep "#CHROM" {output.data_1000g_key} > {output.bim}
        singularity exec --bind {params.bind} {params.sif} grep -Ff {output.SNPs2keep} {output.data_1000g_key} >> {output.bim}
        singularity exec --bind {params.bind} {params.sif} awk 'BEGIN{{FS=OFS="	"}}NF{{NF-=1}};1' < {output.bim} > {output.bim_temp}
        singularity exec --bind {params.bind} {params.sif} grep "##" {output.bim_1000g} > {output.bim}
        singularity exec --bind {params.bind} {params.sif} cat {output.bim_temp} >> {output.bim}

Jobs 1

Input files

/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/indiv_missingness/indiv_missingness.pgen
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/indiv_missingness/indiv_missingness.pvar
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/indiv_missingness/indiv_missingness.psam

Output files

/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/common_snps/snps_data.tsv
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/common_snps/snps_1000g.tsv
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/common_snps/subset_data.pgen
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/common_snps/subset_data.pvar
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/common_snps/subset_data.psam
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/common_snps/subset_1000g.pgen
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/common_snps/subset_1000g.pvar
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/common_snps/subset_1000g.psam

Code

        singularity exec --bind {params.bind} {params.sif} awk 'NR==FNR{{a[$1,$2,$4,$5];next}} ($1,$2,$4,$5) in a{{print $3}}' {input.bim} {params.bim_1000} > {output.snps_1000g}
        singularity exec --bind {params.bind} {params.sif} awk 'NR==FNR{{a[$1,$2,$4,$5];next}} ($1,$2,$4,$5) in a{{print $3}}' {params.bim_1000} {input.bim} > {output.snps_data}
        singularity exec --bind {params.bind} {params.sif} plink2 --threads {threads} --pfile {params.infile} --extract {output.snps_data} --make-pgen 'psam-cols='fid,parents,sex,phenos --out {params.out}
        singularity exec --bind {params.bind} {params.sif} plink2 --threads {threads} --pfile {params.infile_1000g} --extract {output.snps_1000g} --make-pgen --out {params.out_1000g}

Jobs 1

Input files

/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/common_snps/subset_pruned_1000g.pgen
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/common_snps/subset_pruned_1000g.pvar
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/common_snps/subset_pruned_1000g.psam
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/common_snps/subset_pruned_data.pgen

Output files

/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/pca_projection/subset_pruned_1000g_pcs.acount
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/pca_projection/subset_pruned_1000g_pcs.eigenvec.allele
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/pca_projection/subset_pruned_1000g_pcs.eigenvec
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/pca_projection/subset_pruned_1000g_pcs.eigenval

Code

1 2	`singularity exec --bind {params.bind} {params.sif} plink2 --threads {threads} --pfile {params.infile} --freq counts --pca allele-wts --out {params.out}`

Jobs 1

Input files

/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/indiv_missingness/indiv_missingness.pgen
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/indiv_missingness/indiv_missingness.pvar
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/indiv_missingness/indiv_missingness.psam

Output files

/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/check_sex/check_sex.bed
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/check_sex/check_sex.bim
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/check_sex/check_sex.fam
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/check_sex/check_sex.hh
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/check_sex/check_sex.log
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/check_sex/check_sex.nosex
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/check_sex/check_sex.sexcheck
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/check_sex/check_sex.sexcheck.tsv

Code

        singularity exec --bind {params.bind} {params.sif} plink2 --threads {threads} --pfile {params.infile} --make-bed --max-alleles 2 --out {params.out}
        singularity exec --bind {params.bind} {params.sif} plink --threads {threads} --bfile {params.out} --check-sex --out {params.out}
        singularity exec --bind {params.bind} {params.sif} touch {output.nosex}
        singularity exec --bind {params.bind} {params.sif} sed 's/^ \+//g' {output.sexcheck} | singularity exec --bind {params.bind} {params.sif} sed 's/ \+/	/g' > {output.sexcheck_tab}

Jobs 1

Input files

/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/update_sex_ancestry/update_sex.psam

Output files

/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/subset_ancestry/{ancestry}_individuals.psam
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/subset_ancestry/{ancestry}_subset.pgen
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/subset_ancestry/{ancestry}_subset.psam
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/subset_ancestry/{ancestry}_subset.pvar

Code

1
2
3

        singularity exec --bind {params.bind} {params.sif} grep {wildcards.ancestry} {input.psam} > {output.keep}
        singularity exec --bind {params.bind} {params.sif} plink2 --threads {threads} --pfile {params.infile} --keep {output.keep} --max-alleles 2 --make-pgen 'psam-cols='fid,parents,sex,phenos --out {params.out}

Jobs 22

Input files

/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/eagle_prephasing/{ancestry}_chr{chr}_phased.vcf.gz
/directflow/SCCGGroupShare/projects/data/reference_data/1000G_hg38_imputation_ref/hg38/imputation/chr{chr}.m3vcf.gz

Output files

/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/minimac_imputed/{ancestry}_chr{chr}.dose.vcf.gz

Code

1
2

        singularity exec --bind {params.bind} {params.sif} {params.minimac4} --refHaps {input.impute_file}             --haps {input.vcf}             --prefix {params.out}             --format GT,DS,GP             --noPhoneHome             --cpus {threads}             --ChunkLengthMb {params.chunk_length}

Jobs 22

Input files

/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/split_by_chr/{ancestry}_chr_{chr}.vcf.gz
/directflow/SCCGGroupShare/projects/data/reference_data/1000G_hg38_imputation_ref/hg38/phasing/genetic_map/genetic_map_hg38_withX.txt.gz
/directflow/SCCGGroupShare/projects/data/reference_data/1000G_hg38_imputation_ref/hg38/phasing/phasing_reference/chr{chr}.bcf

Output files

/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/eagle_prephasing/{ancestry}_chr{chr}_phased.vcf.gz

Code

1
2

        singularity exec --bind {params.bind} {params.sif} eagle --vcfTarget={input.vcf}             --vcfRef={input.phasing_file}             --geneticMapFile={input.map_file}             --chrom={wildcards.chr}             --outPrefix={params.out}             --numThreads={threads}

Jobs 22

Input files

/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/het_filter/{ancestry}_het_filtered.vcf.gz
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/het_filter/{ancestry}_het_filtered.vcf.gz.csi

Output files

/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/split_by_chr/{ancestry}_chr_{chr}.vcf.gz
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/split_by_chr/{ancestry}_chr_{chr}.vcf.gz.csi

Code

1
2
3

        singularity exec --bind {params.bind} {params.sif} bcftools view -r {wildcards.chr} {input.filtered_vcf} -Oz -o {output.vcf}
        singularity exec --bind {params.bind} {params.sif} bcftools index {output.vcf}

Jobs 1

Input files

/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/het/{ancestry}_het_passed.txt
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/filter_preimpute_vcf/{ancestry}_filtered.vcf.gz

Output files

/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/het_filter/{ancestry}_het_filtered.vcf.gz
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/het_filter/{ancestry}_het_filtered.vcf.gz.csi

Code

        singularity exec --bind {params.bind} {params.sif} bcftools view -S {input.passed_list} {input.vcf} -Oz -o {output.vcf}

        #Index the output file
        singularity exec --bind {params.bind} {params.sif} bcftools index {output.vcf}

Jobs 1

Input files

/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/filter_preimpute_vcf/{ancestry}_filtered.vcf.gz

Output files

/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/het/{ancestry}_filtered_temp.vcf
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/het/{ancestry}_het_failed.inds
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/het/{ancestry}_het.het
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/het/{ancestry}_het_passed.inds
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/het/{ancestry}_het_passed.txt

Code

        singularity exec --bind {params.bind} {params.sif} gunzip -c {input.vcf} | sed 's/^##fileformat=VCFv4.3/##fileformat=VCFv4.2/' > {output.tmp_vcf}
        singularity exec --bind {params.bind} {params.sif} vcftools --vcf {output.tmp_vcf} --het --out {params.het_base}
        singularity exec --bind {params.bind} {params.sif} Rscript {params.script} {output.het} {output.inds} {output.passed} {output.passed_list}

Jobs 1

Input files

/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/vcf_fixref_hg38/{ancestry}_fixref_hg38.vcf.gz

Output files

/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/filter_preimpute_vcf/{ancestry}_tagged.vcf.gz
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/filter_preimpute_vcf/{ancestry}_filtered.vcf.gz
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/filter_preimpute_vcf/{ancestry}_filtered.vcf.gz.csi

Code

        #Add tags
        singularity exec --bind {params.bind} {params.sif} bcftools +fill-tags {input.vcf} -Oz -o {output.tagged_vcf}

        #Filter rare and non-HWE variants and those with abnormal alleles and duplicates
        singularity exec --bind {params.bind} {params.sif} bcftools filter -i 'INFO/HWE > {params.hwe} & F_MISSING < {params.missing} & MAF[0] > {params.maf}' {output.tagged_vcf} |        singularity exec --bind {params.bind} {params.sif} bcftools filter -e 'REF="N" | REF="I" | REF="D"' |        singularity exec --bind {params.bind} {params.sif} bcftools filter -e "ALT='.'" |        singularity exec --bind {params.bind} {params.sif} bcftools norm -d all |        singularity exec --bind {params.bind} {params.sif} bcftools norm -m+any |        singularity exec --bind {params.bind} {params.sif} bcftools view -m2 -M2 -Oz -o {output.filtered_vcf}

        #Index the output file
        singularity exec --bind {params.bind} {params.sif} bcftools index {output.filtered_vcf}

Jobs 1

Input files

/directflow/SCCGGroupShare/projects/data/reference_data/1000G_hg38_imputation_ref/hg38/ref_genome_QC/Homo_sapiens.GRCh38.dna.primary_assembly.fa
/directflow/SCCGGroupShare/projects/data/reference_data/1000G_hg38_imputation_ref/hg38/ref_panel_QC/30x-GRCh38_NoSamplesSorted.vcf.gz
/directflow/SCCGGroupShare/projects/data/reference_data/1000G_hg38_imputation_ref/hg38/ref_panel_QC/30x-GRCh38_NoSamplesSorted.vcf.gz.tbi
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/harmonize_hg38/{ancestry}_harmonised_hg38.vcf.gz

Output files

/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/vcf_fixref_hg38/{ancestry}_fixref_hg38.vcf.gz
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/vcf_fixref_hg38/{ancestry}_fixref_hg38.vcf.gz.csi

Code

        singularity exec --bind {params.bind} {params.sif} bcftools +fixref {input.data_vcf} -- -f {input.fasta} -i {input.vcf} |         singularity exec --bind {params.bind} {params.sif} bcftools norm --check-ref x -f {input.fasta} -Oz -o {output.vcf}

        #Index
        singularity exec --bind {params.bind} {params.sif} bcftools index {output.vcf}

Jobs 1

Input files

/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/harmonize_hg38/{ancestry}.bed
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/harmonize_hg38/{ancestry}.bim
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/harmonize_hg38/{ancestry}.fam

Output files

/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/harmonize_hg38/{ancestry}_harmonised_hg38.vcf.gz
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/harmonize_hg38/{ancestry}_harmonised_hg38.vcf.gz.csi

Code

        singularity exec --bind {params.bind} {params.sif} plink2 --bfile {params.infile} --recode vcf id-paste=iid --chr 1-22 --out {params.out}

        singularity exec --bind {params.bind} {params.sif} bgzip {params.out}.vcf
        singularity exec --bind {params.bind} {params.sif} bcftools index {output.data_vcf_gz}

Jobs 1

Input files

/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/crossmapped_sorted/{ancestry}_crossmapped_sorted.bed
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/crossmapped_sorted/{ancestry}_crossmapped_sorted.bim
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/crossmapped_sorted/{ancestry}_crossmapped_sorted.fam
/directflow/SCCGGroupShare/projects/data/reference_data/1000G_hg38_imputation_ref/hg38/ref_panel_QC/30x-GRCh38_NoSamplesSorted.vcf.gz
/directflow/SCCGGroupShare/projects/data/reference_data/1000G_hg38_imputation_ref/hg38/ref_panel_QC/30x-GRCh38_NoSamplesSorted.vcf.gz.tbi

Output files

/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/harmonize_hg38/{ancestry}.bed
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/harmonize_hg38/{ancestry}.bim
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/harmonize_hg38/{ancestry}.fam

Code

1
2

        singularity exec --bind {params.bind} {params.sif} java -Xmx{resources.java_mem}g -jar {params.jar}            --input {params.infile}            --inputType PLINK_BED            --ref {input.vcf}            --refType VCF            --update-id            --output {params.out}

Jobs 1

Input files

/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/crossmapped/{ancestry}_crossmapped_plink.bed
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/crossmapped/{ancestry}_crossmapped_plink.bim
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/crossmapped/{ancestry}_crossmapped_plink.fam

Output files

/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/crossmapped_sorted/{ancestry}_crossmapped_sorted.bed
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/crossmapped_sorted/{ancestry}_crossmapped_sorted.bim
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/crossmapped_sorted/{ancestry}_crossmapped_sorted.fam

Code

1 2	`singularity exec --bind {params.bind} {params.sif} plink2 --bfile {params.infile} --make-bed --max-alleles 2 --output-chr MT --out {params.out}`

Jobs 1

Input files

/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/subset_ancestry/{ancestry}_subset.pgen
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/subset_ancestry/{ancestry}_subset.psam
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/subset_ancestry/{ancestry}_subset.pvar

Output files

/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/crossmapped/{ancestry}_crossmapped_plink.bed
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/crossmapped/{ancestry}_crossmapped_plink.bim
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/crossmapped/{ancestry}_crossmapped_plink.fam
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/crossmapped/{ancestry}_crossmap_input.bed
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/crossmapped/{ancestry}_crossmap_output.bed
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/crossmapped/{ancestry}_excluded_ids.txt

Code

        singularity exec --bind {params.bind} {params.sif} awk 'BEGIN{{FS=OFS="	"}}{{print $1,$2,$2+1,$3,$4,$5}}' {input.pvar} > {output.inbed}
        singularity exec --bind {params.bind} {params.sif} CrossMap.py bed {params.chain_file} {output.inbed} {output.outbed}
        singularity exec --bind {params.bind} {params.sif} awk '{{print $4}}' {output.outbed}.unmap > {output.excluded_ids}
        singularity exec --bind {params.bind} {params.sif} plink2 --pfile {params.in_plink} --exclude {output.excluded_ids} --make-bed --output-chr MT --out {params.out}
        singularity exec --bind {params.bind} {params.sif} awk -F'	' 'BEGIN {{OFS=FS}} {{print $1,$4,0,$2,$6,$5}}' {output.outbed} > {output.bim}

Jobs 1

Input files

at 0x7f06c0a63d90>
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/update_sex_ancestry/update_sex.psam

Output files

/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/genotype_donor_annotation/genotype_donor_annotation_temp.tsv
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/genotype_donor_annotation/combined_individuals.tsv
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/genotype_donor_annotation/genotype_donor_annotation.tsv

Code

        singularity exec --bind {params.bind} {params.sif} cut -f2,5- {input.updated_psam} | awk 'NR<2{{print $0;next}}{{print $0| "sort -k1,1"}}' > {output.out_temp}
        singularity exec --bind {params.bind} {params.sif} cat {input.individuals} >> {output.combined_individuals}
        singularity exec --bind {params.bind} {params.sif} sed -i '1 i\IID' {output.combined_individuals}
        singularity exec --bind {params.bind} {params.sif} awk -F"	" 'NR==FNR {{a[$1]; next}} $1 in a' {output.combined_individuals} {output.out_temp} | awk 'BEGIN{{FS=OFS="	"}}{{sub("1","M",$2);print}}' | awk 'BEGIN{{FS=OFS="	"}}{{sub("2","F",$2);print}}' > {output.final}
        singularity exec --bind {params.bind} {params.sif} sed -i 's/^IID	SEX	Provided_Ancestry/donor_id	sex	ethnicity_super_population/g' {output.final}
        singularity exec --bind {params.bind} {params.sif} sed -i 's/$/	sceQTL-Gen_hg38_imputation_pipeline	1000g_30x_GRCh38_ref/' {output.final}
        singularity exec --bind {params.bind} {params.sif} sed -i '1s/SangerImputationServer/imputation_method/g' {output.final}
        singularity exec --bind {params.bind} {params.sif} sed -i '1s/1000g_30x_GRCh38_ref/imputation_reference/g' {output.final}

Jobs 1

Input files

/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/het_filter/{ancestry}_het_filtered.vcf.gz
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/het_filter/{ancestry}_het_filtered.vcf.gz.csi

Output files

/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/filter_preimpute_vcf/{ancestry}_het_filtered.vcf
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/filter_preimpute_vcf/{ancestry}_genotypes.imiss
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/genotype_donor_annotation/{ancestry}_individuals.tsv

Code

        singularity exec --bind {params.bind} {params.sif} gunzip -c {input.filtered_vcf} | sed 's/^##fileformat=VCFv4.3/##fileformat=VCFv4.2/' > {output.tmp_vcf}

        singularity exec --bind {params.bind} {params.sif} vcftools --gzvcf {output.tmp_vcf} --missing-indv --out {params.out}

        singularity exec --bind {params.bind} {params.sif} bcftools query -l {input.filtered_vcf} >> {output.individuals}

Jobs 1

Input files

at 0x7f06c09dbae8>

Output files

/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/vcf_merged_by_ancestries/{ancestry}_imputed_hg38.vcf.gz
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/vcf_merged_by_ancestries/{ancestry}_imputed_hg38.vcf.gz.csi

Code

1
2
3

        singularity exec --bind {params.bind} {params.sif} bcftools concat -Oz {params.files_begin} > {output.combined}
        singularity exec --bind {params.bind} {params.sif} bcftools index {output.combined}

Jobs 1

Input files

/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/vcf_all_merged/imputed_hg38_R2_0.3_MAF0.05_exons_complete_cases.recode.vcf

Output files

/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/vcf_4_demultiplex/imputed_hg38_R2_0.3_MAF0.05_exons_sorted.vcf

Code

1
2

        singularity exec --bind {params.bind} {params.sif} java -Xmx{resources.java_mem}g -Xms{resources.java_mem}g -jar /opt/picard/build/libs/picard.jar SortVcf             I={input.complete_cases}             O={output.complete_cases_sorted}

Jobs 1

Input files

/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/vcf_all_merged/imputed_hg38.vcf.gz

Output files

/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/vcf_all_merged/imputed_hg38_info_filled.vcf.gz
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/vcf_all_merged/imputed_hg38_R2_0.3_MAF0.05.vcf.gz
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/vcf_all_merged/imputed_hg38_R2_0.3_MAF0.05_exons.recode.vcf
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/vcf_all_merged/imputed_hg38_R2_0.3_MAF0.05_exons_complete_cases.recode.vcf

Code

        ##### Add all the info fields
        singularity exec --bind {params.bind} {params.sif} bcftools +fill-tags -Oz --output {output.info_filled} {input}

        ##### Filter the Imputed SNP Genotype by Minor Allele Frequency (MAF) and INFO scores #####
        singularity exec --bind {params.bind} {params.sif} bcftools filter --include 'MAF>=0.05 & R2>=0.3' -Oz --output {output.qc_filtered} {output.info_filled}


        singularity exec --bind {params.bind} {params.sif} vcftools             --gzvcf {output.qc_filtered}             --max-alleles 2             --remove-indels             --bed {params.bed}             --recode             --recode-INFO-all             --out {params.out}

        singularity exec --bind {params.bind} {params.sif} vcftools --recode --recode-INFO-all --vcf {output.location_filtered} --max-missing 1 --out {params.complete_out}

Jobs 1

Input files

at 0x7f06c09dbea0>

Output files

/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/vcf_all_merged/imputed_hg38.vcf.gz
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/vcf_all_merged/imputed_hg38.vcf.gz.csi

Code

        if [[ $(ls -l {input.vcfs} | wc -l) > 1 ]]
        then
            singularity exec --bind {params.bind} {params.sif} bcftools merge -Oz {input.vcfs} > {output.combined}
        else
            cp {input.vcfs} {output.combined}
        fi
        singularity exec --bind {params.bind} {params.sif} bcftools index {output.combined}

Jobs 1

Input files

/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/vcf_all_merged/imputed_hg38_info_filled.vcf.gz
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/vcf_all_merged/imputed_hg38_R2_0.3_MAF0.05.vcf.gz
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/vcf_4_demultiplex/imputed_hg38_R2_0.3_MAF0.05_exons_sorted.vcf

Output files

/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/metrics/Number_SNPs.png

Code

1 2	`singularity exec --bind {params.bind} {params.sif} Rscript {params.script} {params.basedir} {params.outdir}`

Jobs 1

Input files

/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/check_sex/check_sex.sexcheck.tsv
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/pca_sex_checks/check_sex_update_remove.tsv
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/indiv_missingness/indiv_missingness.psam
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/pca_sex_checks/ancestry_update_remove.tsv

Output files

/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/metrics/sex_summary.png
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/Imputation_Urmo/Test18/results/metrics/ancestry_summary.png

Code

1 2	`singularity exec --bind {params.bind} {params.sif} Rscript {params.script} {params.basedir} {params.outdir}`

Workflow

Ancestry

Ancestry and Sex Summary

SNP Numbers

Statistics