Dear community members,

I need to genotype 6 millions of array markers from a BAM WGS file.

It works perfectly for substitutions, e.g., ref allele C, alt allele G,, but indels are problematic - the "format" of array variants is a bit different, for example, ref/alt alleles for array can be:

ACG ACGACG

which would be just insertion of ACG in VCF file from WGS.

Do you know any tools that can genotype these weird array variants in WGS?