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broadinstitute / gatk

Official code repository for GATK versions 4 and up
https://software.broadinstitute.org/gatk
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Remove PyVCF, biopython dependencies #4465

Open lucidtronix opened 6 years ago

lucidtronix commented 6 years ago

maybe we can keep pysam?

cmnbroad commented 6 years ago

@lucidtronix Whats the motivation for wanting to keep it ? I think we really want to avoid it if at all possible, but if there is a reason its necessary let us know and we can discuss.

cmnbroad commented 6 years ago

Also pysam. Depends on https://github.com/broadinstitute/gatk/issues/4533, https://github.com/broadinstitute/gatk/issues/4534 and https://github.com/broadinstitute/gatk/issues/4535.