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From: Sébastien L. <seb...@in...> - 2015-04-16 09:36:52
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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)
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