add MAF

Snakefile

@@ -72,7 +72,7 @@ rule vcf_to_dosages:
         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
         echo "add computing MAFs ..."
-        bcftools $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
         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