VCFtools doesn’t keep any variants using GATK output

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:

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 … “

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