I have two cohorts and want to joint analyze them, each cohort is from a different project and thus the library and sequencing configurations are different. Should I run hipstr separately for each cohort and merge the vcf, or run two cohorts together? I'm planning to do "Use de novo stutter estimation + STR calling with de novo allele generation".
And if the suggestion is to run hipstr on the two cohorts together, is there a strategy to analyze large amount of deeply sequence WGS samples, say 1000 samples at 100x without downloading all bam files to local?
Hi,
I have two cohorts and want to joint analyze them, each cohort is from a different project and thus the library and sequencing configurations are different. Should I run hipstr separately for each cohort and merge the vcf, or run two cohorts together? I'm planning to do "Use de novo stutter estimation + STR calling with de novo allele generation".
And if the suggestion is to run hipstr on the two cohorts together, is there a strategy to analyze large amount of deeply sequence WGS samples, say 1000 samples at 100x without downloading all bam files to local?
Thanks!