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GRCh37/hg19: should I re-process my BAMs?
I have a human exome experiment on which I am using hg19 resources (reference, targets, dbSNP, ... the whole shebang). I want to add some 1000Genomes exomes to this experiment, but the available BAMs are from GRCh37.
Is there a tool to port the BAMs from GRCh37 to hg19, and to continue with that? Maybe LiftOver?
Do you rather recommend re-processing the 1000Genomes BAMs on hg19? Would that mean regenerate FASTQs and re-do the whole map/MarkDup/IndelReal/BQSR steps?
For now, I have worked on the original BAMs but have renamed all the classical chromosomes from "1" to "chr1" and I got rid of the mitochondrial chromosome and all other contigs (got rid of these contigs also in the resources to avoid GATKs complaints on missing contigs). How bad would you think that is based on the differences you know between GRCh37 and hg19?
Thanks a lot for your help!