Hello,
I'm rather new to variant calling and had a question regarding this process on NGS data performed on a specific locus.
I sequenced the PCR amplicon of a bunch of samples in a pool together. Let's say I have 20 samples which were all diploid.
I expect some SNPs in some of the alleles but it's also possible that there is more than 1 SNP in 1 allele.
Is it possible to do a variant calling process that will 'group' the two SNPs in 1 allele together? I looked into it a bit and I maybe found HaplotypeCaller, but I'm unsure if this will do the trick.
My apologies if this is a stupid question.
Kind regards