Vcf files: a little problem applying filters

[jmatés]

Hi all! It's my first post in SeqAnswers forum. This site is awesome !

I'm struggling with a .vcf file that I'm trying to filter based on QUAL and DP fields. When I apply the filter and check if everything went well, I find that there are many variations that have not been filtered.

I've used this command for generating and filtering the file:

samtools mpileup -uf hg19.fa myfile.bam | bcftools view -bvcg - > var.raw.bcf

bcftools view var.raw.bcf | /usr/share/samtools/vcfutils.pl varFilter -D500 > myfile.vcf

cat myfile.vcf | vcf-annotate --filter Qual=30/MinDP=20 > myfile_filtered.vcf

Here is a fragment of my file after being filtered. I've narrowed it for brevity:

#CHROM POS ID REF ALT QUAL FILTER INFO
chr1 237993724 . C T 86 . DP=14;VDB=0.00(...)

chr1 237996076 . C G 158 . DP=166;VDB=0.0955(...)

chr1 237996661 . C G 3.54 . DP=31;VDB=0.0792(...)

chr1 237997087 . A G 225 . DP=220;VDB=0.0955(...)

chr1 237997254 . C T 108 . DP=255;VDB=0.0733(...)

chr3 8775457 . G A 44 PASS DP=50;VDB=0.0656(...)

As you can see the first entry shoudn't pass the filter because the DP field is under the filter value, and the third entry has a bad quality. The others although meet the filter specifications are not tagged with a “PASS” label.

I'm pretty sure that there isn't any problem with the vcf file before being filtered and I've been unable to find a threat with an issue like this... any help would be much appreciated.

Thanks in advance!

[aeonsim]

Not sure what's going on there but there are a number of other filtering tools that I'd recommend over vcf-annotate.

http://snpeff.sourceforge.net/SnpSift.html is very powerful and feature rich and runs pretty much everywhere being java based.
Or
https://github.com/ekg/vcflib a clean set of tools for manipulating VCF files, vcffilter would do what you want.

[jmatés]

Not sure what's going on there but there are a number of other filtering tools that I'd recommend over vcf-annotate.

http://snpeff.sourceforge.net/SnpSift.html is very powerful and feature rich and runs pretty much everywhere being java based.
Or
https://github.com/ekg/vcflib a clean set of tools for manipulating VCF files, vcffilter would do what you want.

Thank you aeonsim! Giving them a look immediately.