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Update vector spec to reflect removal of calmd and usage of Picard SetNmMdAndUqTags tool #17

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gbggrant opened this issue May 8, 2020 · 1 comment
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Update vector spec to reflect removal of calmd and usage of Picard SetNmMdAndUqTags tool #17

gbggrant opened this issue May 8, 2020 · 1 comment
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gbggrant commented May 8, 2020

The initial version of the pipeline generated an output bam that failed ValidateSamFile due to a difference between the implementations of the calculation of the value of the NM tag in samtool's calmd tool and that in picard's ValidateSamFile tool. See: samtools/samtools#717 (comment)

After discussion with @alimanfoo and others, and with the understanding that the NM tag is not used elsewhere (particularly in gatk 3's UnifiedGenotyper), the decision was made to remove the usage of calmd and replace it with Picard's SetNmMdAndUqTags tool.
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The spec has been updated and the code changed

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