We've moved!
This site is now read-only. You can find our new documentation site and support forum for posting questions here.
Be sure to read our welcome blog!

about combine GVCFs

after filtering the vcf files with ISHet Filter, I am using the command CombineGVCFs as follows:
.././gatk CombineGVCFs -R reference.fasta --variant filtered1.g.vcf --variant filtered2.g.vcf --variant filtered3.snps.g.vcf -O combined.vcf

The input vcf files have thousands of SNPs but after combining these files, there is no SNP in the OUTPUT file. why is so? Kindly guide me .

I am using vGATK4.1.0.0

Answers

Sign In or Register to comment.