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impute-gene-expression
impute-gene-expression
Commit e211fe26 authored by Kevin Kunzmann's avatar Kevin Kunzmann
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add MAF

parent 148ef2a8
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...@@ -71,8 +71,8 @@ rule vcf_to_dosages: ...@@ -71,8 +71,8 @@ rule vcf_to_dosages:
mkdir -p $prefix mkdir -p $prefix
echo "decompress and filter out: 'MAF[0]<{config[min_MAF]} | INFO<{config[min_INFO]} | TYPE!="snp" | N_ALT!=1' ..." echo "decompress and filter out: 'MAF[0]<{config[min_MAF]} | INFO<{config[min_INFO]} | TYPE!="snp" | N_ALT!=1' ..."
bcftools filter -e 'MAF[0]<{config[min_MAF]} | INFO<{config[min_INFO]} | TYPE!="snp" | N_ALT!=1' {input.vcf_gz_file} > $prefix/chr{wildcards.i}_.vcf bcftools filter -e 'MAF[0]<{config[min_MAF]} | INFO<{config[min_INFO]} | TYPE!="snp" | N_ALT!=1' {input.vcf_gz_file} > $prefix/chr{wildcards.i}_.vcf
echo "add computing MAFs ..." echo "add MAFs ..."
bcftools +fill-tags $prefix/chr{wildcards.i}.vcf_ > $prefix/chr{wildcards.i}.vcf bcftools +fill-tags $prefix/chr{wildcards.i}_.vcf > $prefix/chr{wildcards.i}.vcf
rm $prefix/chr{wildcards.i}_.vcf rm $prefix/chr{wildcards.i}_.vcf
echo 'querying dosages ...' echo 'querying dosages ...'
bcftools query -f '%CHROM %ID %POS %REF %ALT %INFO/MAF [%DS ]\n' $prefix/chr{wildcards.i}.vcf > $prefix/chr{wildcards.i}.dosage.txt bcftools query -f '%CHROM %ID %POS %REF %ALT %INFO/MAF [%DS ]\n' $prefix/chr{wildcards.i}.vcf > $prefix/chr{wildcards.i}.dosage.txt
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