Filtering with vcftools by QUAL, Does not produce an output file

Question

[Michal Nevo]

Hello, I want to filter my VCF file by QUAL >10 . AND GET AN OUTPUT VCF FILE so I could continue with my pipeline

When I try to use this command there are no errors but no result either:

vcftools --vcf $VCF_IN --minQ $10 --recode-INFO-all > $VCF_OUT

And when I use bcftools query it outputs only the records..but it is not an vcf file..

bcftools query -i 'QUAL>10' -f '%CHROM\t%POS\t%REF\t%ALT\t%QUAL\t%FILTER\t%INFO\t%FORMAT\n' $VCF_IN --output $VCF_OUT

VCF_OUT:

NC_048323.1     461     G       T       28.1057 . AB=0;ABP=0;AC=4;AF=1;AN=4;AO=2;CIGAR=1X;DP=2;DPB=2;DPRA=0;EPP=3.0103;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=29;MQMR=0;NS=1;NUMALT=1;ODDS=5.46822;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=51;QR=0;RO=0;RPL=0;RPP=7.35324;RPPR=0;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=0;SRP=0;SRR=0;TYPE=snp        GT:DP:AD:RO:QR:AO:QA    1/1/1/1:2:0,2:0:0:2:51 

[Michal Nevo]

What is the standard QUAL filtering? 10/15/20/30?

Answer 1

[4galaxy77]

bcftools query doesn't output a vcf, it outputs a formatted string. If you want to filter the vcf, just do bcftools view -i 'QUAL>10' $VCF_IN --output $VCF_OUT.

And vcftools is deprecated, use bcftools instead.

[Michal Nevo]

Thank you! it is working:)