HaplotypeCaller - treatment of scaffolds
1 BAM = 1 individual
my question is regarding the HaplotypeCaller and scaffolds in a BAM file.
When I want to do the individual SNP-calling procedure (--emitRefConfidence GVCF) before the Joint Genotyping,
I found that with my number of scaffolds the process is computationally quite costy.
I now ran for every BAM the HaplotypeCaller just for a single scafflod (by using -L)
Question is: Do you see any downside in this approach regarding the result quality?
Or are the scaffolds treated independently anyways and my approach is fine?
The next step would be to combine the gvcfs to a single one again (corresponding to the original BAM)
and then do joint genotyping on a cohort of gvcfs (-> cohort of individuals)
Thanks a lot!