vcftools minDP filter not working for samtools genotype calling output
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4.8 years ago
Jautis ▴ 570

Hello, I've called genotypes using samtools/bcftools and am now trying to filter the genotype calls based on mean depth (DP > 10). However, when I use the minDP filter in vcftools nothing happens. Alternately, the minQ filter seems to be working well. Any ideas why this is or what I could do?

Here's the command I am trying to use: vcftools --gzvcf my_file.vcf.gz --minQ 30 --minDP 10 --recode-INFO-all --recode --out filtered.

In case it helps, here is a few sites from my pre-filtered VCF. Thanks!

> #CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  sample 
> chr1    864     .       C       G       9.6787  .       DP=1    GT:PL   0/1:27,3,0 
> chr1    11322   .       A       G       11.5001 .       DP=1    GT:PL   0/1:29,3,0
> chr1    22289   .       G       T       180     .       DP=56   GT:PL   1/1:197,169,0

There's some other information for each site under info (e.g. ;SGB=-0.379885;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=0,0,0,1;MQ=60) which I've removed from this example to keep everything more clean.

genotype filtering SNP SNP-calling • 1.8k views
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vcftools is deprecated. Use bcftools instead.

bcftools view -i 'DP>=10 && MQ>=30' my_file.vcf.gz > out.vcf
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Thanks! I was not aware of that.

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