Hi guys!
I'm having trouble using vcftools to filter snp through GATK output.
For information, I used the command HaplotypeCaller to 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 VariantFiltration 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 wrong? 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 ...
Thank you very much !! I didn't pay attention to this detail... Now it worked!!