I have a vcf file with some snps. the vcf file contains multiple samples.
I used freebayes, BCFtools and GATK.
I would like to Filter on Quality and depth.
For Quality i use MINQ in vcftools.
vcftools --gzvcf raw.vcf.gz --minQ 30 --recode --recode-INFO-all --out filtered_MINQ_30
When using this filter i encounter no problem with any vcf file. Everything goes fine. All sites that have a quality less than 30 are filtered out.
However when I want to filter on Depth(DP) not a single variant gets filtered out. even when i think they should.
i use the following command line:
vcftools --gzvcf raw.vcf.gz --minDP 200 --recode --recode-INFO-all --out raw.dp200
the numbers of sites i have before and after are the same.
This is how one site looks like in my VCF file.
CG_Chr01 307 . C T 96.3 . AC=5;AF=0.192;AN=26;BaseQRankSum=0.739;ClippingRankSum=0.000;DP=73;ExcessHet=0.0570;FS=0.000;InbreedingCoeff=0.4884;MLEAC=3;MLEAF=0.115;MQ=34.29;MQRankSum=0.335;QD=34.24;ReadPosRankSum=-0.904;SOR=0.340 GT:AD:DP:GQ:PL 0/0:5,0:5:15:0,15,225 0/0:3,0:3:9:0,9,135 0/0:3,0:3:9:0,9,127 0/1:3,1:4:25:25,0,103 0/0:3,0:3:12:0,12,171 ./.:.:.:.:../.:.:.:.:. ./.:0,1:1:3:36,3,0 0/0:7,0:7:21:0,21,278 ./.:.:.:.:. ./.:.:.:.:. 0/0:7,0:7:24:0,24,360 0/0:9,0:9:27:0,27,398 0/0:8,0:8:24:0,24,326 ./.:0,2:2:6:90,6,0 ./.:.:.:.:. 0/0:10,0:10:30:0,30,430 ./.:.:.:.:. ./.:2,0:2:6:0,6,79
this particular example is from a vcf file created using GATK HaplotypeCaller. but i have the same problem with vcf files created from Freebayes and BCFtools.
Can someone tell me what i am doing wrong or i am overlooking?
I don't know why it doesn't work well, but maybe you could try another tool to filter on depth (ex : snpSift http://snpeff.sourceforge.net/SnpSift.html )
Thank you, I'll look into it.
in the mean time i for the problem solved by using vcffilter