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which file to use as input to DepthOfCoverage?
Hello GATK team,
I'm running the Best Practice pipeline, and I would like to do some coverage calculation on my samples.
I want to use DepthOfCoverage, but I can't decide which bam file to use - the original one, the one after BQSR stage (right before HC) or the bamout of HC?
The point is that the first two files don't contain the reads as they were mapped in the variant calling, since the HC changes the mapping dramatically. The bamout contains haplotypes, and therefor reads are merged together, and the coverage might look lower than the one that uses the reads.
What do you recommend?