bugfix

Snakefile

@@ -70,15 +70,13 @@ rule vcf_to_dosages:
         echo "extracting and computing MAFs ..."
         bcftools +fill-tags {inputs.vcf_gz_file} > $prefix/chr{wildcards.i}.vcf
         echo 'querying dosages ...'
-        bcftools query -e 'MAF[0]<{config[min_MAF]} | INFO<{config[min_INFO]} | TYPE!="snp" | N_ALT!=1' -f '%CHROM %ID %POS %REF %ALT %INFO/MAF [%DS ]\n' $prefix/chr{wildcards.i}.vcf > $prefix/chr{wildcards.i}.dosage.txt
+        bcftools query -e 'MAF[0]>{config[min_MAF]} | INFO>{config[min_INFO]} | TYPE!="snp" | N_ALT!=1' -f '%CHROM %ID %POS %REF %ALT %INFO/MAF [%DS ]\n' $prefix/chr{wildcards.i}.vcf > $prefix/chr{wildcards.i}.dosage.txt
         echo 'compressing ...'
         gzip $prefix/chr{wildcards.i}.dosage.txt
         rm $prefix/chr{wildcards.i}.vcf
         printf "done.\n\r\n\r"
         """
 
-bcftools query -e 'MAF[0]<0.01 | INFO<{config[min_INFO]} | TYPE!="snp" | N_ALT!=1' -f '%CHROM %ID %POS %REF %ALT %INFO/MAF [%DS ]\n' $prefix/chr{wildcards.i}.vcf > $prefix/chr{wildcards.i}.dosage.txt
-
 # extract sample file for PrediXcan
 rule generate_samples_file:
     input: