VCFtools doesn't keep any variants using GATK output
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Entering edit mode
9 months ago
fcarolinebe ▴ 40

Hi guys!

I'm having trouble using vcftools to filter snp through GATK output.

For infomation, i used the command HaplotypeCallerto make SNP-calling of 12 samples ; i used the CombineGVCFs to join the 12 VCFS and make the joint call after merging the vcf files; i used the VarianFiltration for a initial filtration.

Now, i want to make a filtration using VCFtools, for this, i used the command :

vcftools --vcf output_gatk.vcf --remove-indels --recode --recode-INFO-all --out SNPs_gatk_only

But, after the filter, the VCFtools doesn't keep any variant, like this:

"After filtering, kept 12 out of 12 Individuals
Outputting VCF file...
After filtering, kept 0 out of a possible 68599004 Sites
No data left for analysis!
Run Time = 438.00 seconds"

Am I doing something wrorg?

my VCF input has a header like this:

CHROM POS ID REF ALT QUAL FILTER INFO FORMAT T1R2-6H T1R3-24H T1R3-6H T1R6-24H T1R7-24H ...

LG1 1 . G <NON_REF> . PASS END=14 GT:DP:GQ:MIN_DP:PL ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ...

LG1 15 . A G,<NON_REF . PASS END=31 GT:DP:GQ:MIN_DP:PL ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:1:3:1:0,3,19 ... "

gatk. vcftools snps filter • 486 views
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1
Entering edit mode
9 months ago

you're working with a GVCF file. A gvcf should be first post-processed with "gatk GenotypeGVCFs"

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Thank you very much !! I didn't pay attention to this detail... Now it worked!!

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