[Vcftools-help] bcftools apply-filters

[Sébastien L. <seb...@in...>]

Hi,

Maybe I misunderstand, but I have not been able to filter my records :

bcftools query -f '%FILTER\n' 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 '%FILTER\n' | sort | uniq -c
   24009 PASS

for VQSR* filters I can't
bcftools view infile.vcf.gz -f VQSRTrancheSNP99.90to100.00 \
	| bcftools query -f '%FILTER\n' | 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
Inserm U1078, Génétique, Génomique fonctionnelle et Biotechnologies
46 rue Félix Le Dantec
CS 51819
29218 BREST CEDEX 2
Tel. 02.98.22.34.08 (EFS)
Tel. 02.98.01.82.37 (UBO)