Hi, I am trying to filter a vcf file so that I only get indels from it. I am using vcftools with the following command:
vcftools --vcf NIST_RTG_PlatGen_merged_highconfidence_v0.2_Allannotate.vcf --max-alleles 2 --min-alleles 2 --keep-only-indels --recode --recode-INFO-all --out indels
I get the following error:
Error: Flag Type must have 0 entries: ID=isPolymorphic,Number=1,Type=Flag,Description="Sites that are polymorphic in the CEPH1493 pedigree
First time I see this kind of error, I have been filtering vcf files without problems until now. Any idea why vcftools it not filtering this particular vcf?