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fix: .nosex missing issue (Issue 349) #356

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Nov 21, 2024
Merged

fix: .nosex missing issue (Issue 349) #356

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96 changes: 28 additions & 68 deletions src/cgr_gwas_qc/workflow/modules/plink.smk
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Original file line number Diff line number Diff line change
Expand Up @@ -45,16 +45,10 @@ rule sample_call_rate_filter:
mem_mb=lambda wildcards, attempt: attempt * 1024,
time_hr=lambda wildcards, attempt: attempt**2,
shell:
"plink "
"--bed {input.bed} "
"--bim {input.bim} "
"--fam {input.fam} "
"--mind {params.mind} "
"--make-bed "
"--threads {threads} "
"--memory {resources.mem_mb} "
"--out {params.out_prefix}"

"""
plink --bed {input.bed} --bim {input.bim} --fam {input.fam} --mind {params.mind} --make-bed --threads {threads} --memory {resources.mem_mb} --out {params.out_prefix}
touch {output.nosex}
"""

rule snp_call_rate_filter:
input:
Expand All @@ -78,16 +72,10 @@ rule snp_call_rate_filter:
mem_mb=lambda wildcards, attempt: attempt * 1024,
time_hr=lambda wildcards, attempt: attempt**2,
shell:
"plink "
"--bed {input.bed} "
"--bim {input.bim} "
"--fam {input.fam} "
"--geno {params.geno} "
"--make-bed "
"--threads {threads} "
"--memory {resources.mem_mb} "
"--out {params.out_prefix}"

"""
plink --bed {input.bed} --bim {input.bim} --fam {input.fam} --geno {params.geno} --make-bed --threads {threads} --memory {resources.mem_mb} --out {params.out_prefix}
touch {output.nosex}
"""

rule maf_filter:
"""Filter SNPs based on minor allele frequency."""
Expand Down Expand Up @@ -147,16 +135,10 @@ rule ld_filter:
resources:
mem_mb=lambda wildcards, attempt: attempt * 1024,
shell:
"plink "
"--bed {input.bed} "
"--bim {input.bim} "
"--fam {input.fam} "
"--extract {input.to_keep} "
"--make-bed "
"--threads {threads} "
"--memory {resources.mem_mb} "
"--out {params.out_prefix}"

"""
plink --bed {input.bed} --bim {input.bim} --fam {input.fam} --extract {input.to_keep} --make-bed --threads {threads} --memory {resources.mem_mb} --out {params.out_prefix}
touch {output.nosex}
"""

rule snps_only_filter:
"""Exclude all variants with one or more multi-character allele codes"""
Expand Down Expand Up @@ -261,16 +243,10 @@ rule remove_ids:
resources:
mem_mb=lambda wildcards, attempt: attempt * 1024,
shell:
"plink "
"--bed {input.bed} "
"--bim {input.bim} "
"--fam {input.fam} "
"--remove {input.to_remove} "
"--make-bed "
"--threads {threads} "
"--memory {resources.mem_mb} "
"--out {params.out_prefix}"

"""
plink --bed {input.bed} --bim {input.bim} --fam {input.fam} --remove {input.to_remove} --make-bed --threads {threads} --memory {resources.mem_mb} --out {params.out_prefix}
touch {output.nosex}
"""

rule keep_bfile:
"""Tell snakemake to keep the file.
Expand Down Expand Up @@ -298,15 +274,10 @@ rule keep_bfile:
resources:
mem_mb=lambda wildcards, attempt: attempt * 1024,
shell:
"plink "
"--bed {input.bed} "
"--bim {input.bim} "
"--fam {input.fam} "
"--make-bed "
"--threads {threads} "
"--memory {resources.mem_mb} "
"--out {params.out_prefix}"

"""
plink --bed {input.bed} --bim {input.bim} --fam {input.fam} --make-bed --threads {threads} --memory {resources.mem_mb} --out {params.out_prefix}
touch {output.nosex}
"""

################################################################################
# Converters
Expand All @@ -332,16 +303,10 @@ rule rename_ids:
resources:
mem_mb=lambda wildcards, attempt: attempt * 1024,
shell:
"plink "
"--bed {input.bed} "
"--bim {input.bim} "
"--fam {input.fam} "
"--update-ids {input.id_map} "
"--make-bed "
"--threads {threads} "
"--memory {resources.mem_mb} "
"--out {params.out_prefix}"

"""
plink --bed {input.bed} --bim {input.bim} --fam {input.fam} --update-ids {input.id_map} --make-bed --threads {threads} --memory {resources.mem_mb} --out {params.out_prefix}
touch {output.nosex}
"""

rule bed_to_ped:
input:
Expand Down Expand Up @@ -418,15 +383,10 @@ rule ld:
resources:
mem_mb=lambda wildcards, attempt: attempt * 1024,
shell:
"sleep 10 && plink "
"--bed {input.bed} "
"--bim {input.bim} "
"--fam {input.fam} "
"--indep-pairwise 50 5 {params.r2} "
"--threads {threads} "
"--memory {resources.mem_mb} "
"--out {params.out_prefix}"

"""
sleep 10 && plink --bed {input.bed} --bim {input.bim} --fam {input.fam} --indep-pairwise 50 5 {params.r2} --threads {threads} --memory {resources.mem_mb} --out {params.out_prefix}
touch {output.nosex}
"""

rule miss:
"""Runs ``plink`` missingness statistics.
Expand Down
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