Re: [Vcftools-help] bcftools apply-filters

[pd3 <pd...@sa...>]

 

Hi Sébastien, 

your commands look fine, this is how it's supposed to work. However, I
was not able to reproduce the problem. Could you provide a small test
case? 

Cheers, 

Petr 

On 2015-04-16 11:36, Sébastien Letort wrote: 

> Hi,
> 
> Maybe I misunderstand, but I have not been able to filter my records :
> 
> bcftools query -f '%FILTERn' infile.vcf.gz | sort | uniq -c
> 345428 .
> 24009 PASS
> 23087 VQSRTrancheINDEL99.00to99.90
> 2255 VQSRTrancheINDEL99.90to100.00
> 
> To have only PASS, it's ok
> bcftools view infile.vcf.gz -f PASS 
> | bcftools query -f '%FILTERn' | sort | uniq -c
> 24009 PASS
> 
> for VQSR* filters I can't
> bcftools view infile.vcf.gz -f VQSRTrancheSNP99.90to100.00 
> | bcftools query -f '%FILTERn' | sort | uniq -c
> 345428 .
> 
> my header
> bcftools view infile.vcf.gz -h | grep FILTER=
> ##FILTER=<ID=PASS,Description="All filters passed">
> ##FILTER=<ID=LowQual,Description="Low quality">
> ##FILTER=<ID=VQSRTrancheINDEL99.00to99.90,Description="Truth sensitivity 
> tranche level for INDEL model at VQS Lod: -4.1798 <= x < -0.7584">
> ##FILTER=<ID=VQSRTrancheINDEL99.90to100.00+,Description="Truth 
> sensitivity tranche level for INDEL model at VQS Lod < -915.6166">
> ##FILTER=<ID=VQSRTrancheINDEL99.90to100.00,Description="Truth 
> sensitivity tranche level for INDEL model at VQS Lod: -915.6166 <= x < 
> -4.1798">
> 
> Those filters are generated with VQSR method by GATK programs.
> 
> bcftools -v
> bcftools 1.2
> Using htslib 1.2.1
> 
> thanks,
> 
> -- 
> Sébastien Letort - bio-informaticien
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