rajitz

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rajitz
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  • Hi Bhanu, Thanks for the helpful clarifications. For the criteria, even though we don't have hard cutoffs, could you please provide a one-line summary for each one of them in this context? For example, I've heard about "trimming" in terms of ad…
  • Actually with --emitDroppedReads we could be looking at all down-sampled and uninformative reads also in addition to filtered, trimmed and those having realignment failure. Would be great to know more about all these criteria in this context. Th…
  • Thanks for the prompt response. Is there any other way meanwhile to see why certain reads are getting dropped? The documentation for v 3.8 at https://software.broadinstitute.org/gatk/documentation/tooldocs/3.8-0/org_broadinstitute_gatk_tools_walke…
  • Hi, it would really be helpful to have the --emitDroppedReads flag in GATK HaploTypeCaller version 4. Is this expected to be incorporated any time soon? Thanks.