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3.7 years ago
German.M.Demidov
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2.9k
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?
