Filtering VCF file

[JadeB]

Hi,

I'm currently trying to filter my VCF file. I'm working on mtDNA, so I'd like to exclude heterozygous SNP. To do so, I'v tried to use bcftools filter and bcftools query, but I don't manage to keep the GT 1/1 data.

More precisely :

bcftools filter -s LowQual -e '%QUAL<20 || DP>1200 || GT!="1/1"' data.vcf > data_filt.vcf

answers : "No such INFO field: GT"

bcftools filter -s LowQual -e '%QUAL<20 || DP>1200 || FORMAT/GT!="1/1"' data.vcf > data_filt.vcf

answers : " Error: the tag "INFO/AT/GT" is not defined in the VCF header"

bcftools filter -s LowQual -e '%QUAL<20 || DP>1200 || FMT/GT!="1/1"' data.vcf > data_filt.vcf

Answers : No error message, I've a new vcf file, but data are not correctly filtered, all of them are LowQual identified (and all pass if I change != to ==)

Do you have any idea how I could filter my data ? (except something like cat data.vcf | grep 1/1 > data_filt.vcf)

I'm using bcftools 0.2.0-rc8-5-g0e06231, samtools 1.1.

EDIT : no more problem with bcftools 1.1