Hi GATK Team,
I was looking at the Tool page for the 188.8.131.52 HaplotypeCaller found at https://gatk.broadinstitute.org/hc/en-us/articles/4414586765723?page=1#comment_4638698103451
I noticed the message "Input bam file(s) from which to make variant calls" in the Input subsection. Further down, I noticed in the Haplotype Specific Arguments section that the --input argument can take CRAM/SAM/BAM files as input. I was wondering if the program has a preference for input file type? By that I mean, "under the hood" does the program have to do some kind of conversion between file types if one input is offered versus another? Is it computationally more efficient to give the program one type over the others?
Partners Personal Medicine (MGB)
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