Hi,
How would one interpret SNP calling results when applying reads from a polyploid plant, using diploid caller like samtools or default diploid option of GATK?
I'm able to get SNP calls, but do the callers just take the two most common alleles (ref and next most common alt)?
What should I be most careful about when interpreting the results, and especially the confidence values?
Thanks
How would one interpret SNP calling results when applying reads from a polyploid plant, using diploid caller like samtools or default diploid option of GATK?
I'm able to get SNP calls, but do the callers just take the two most common alleles (ref and next most common alt)?
What should I be most careful about when interpreting the results, and especially the confidence values?
Thanks
Comment