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Would it matter a lot to do recalibration before usage of hc? If yes, it's worth to do realignment before recalibration to reduce no of snv's, I guess. I'm searching for variants in one of not too much known genomes. What I've got is 30x coverage and haploids I work on. I did realignment and recalibration but I'm thinking if it helps me in anything while I don't know any obvious snp sites. And if it's not better to use haplotypecaller stright away after mapping and then do the recalibration with a bunch of best quality variants?
Please, help in that matter.