Laura Gauthier

@tfenne a Terra workspace prototype I started ran the cohort caller in 39 shards and took 2.5 hrs, which ended up being $3.25. This was on 1000G exomes where at...

Yeah, there is a reblocking bug in 4.2.5.0. It's fixed in master, but we are waiting on a Google NIO fix for requester-pays buckets before we release a new version....

This is a hot topic recently, so I already have a doc to compare and contrast: https://docs.google.com/document/d/1qws0owSEc0XGcZGAcxmBOEk8fiWS1Dnv4tvHNgC_xVU/edit?usp=sharing Gnarly is still a "beta" tool. I wanted to add some way to...

Replaces #7797

@droazen Are you thinking String with count=1 and then DIY parsing? Despite _years_ of discussions, we never made any progress on lists of lists in the VCF spec.

It looks like that's just what Don did in #6858

See also https://broadinstitute.atlassian.net/browse/PO-47848

@spatel-gfb another option that should improve performance is to run the GATK GVCF postprocessing tool ReblockGVCF on all of your input GVCFs. That tool merges reference blocks (which BAF calculation...

The VCF sequence dictionary does contain a chrX -- is that enough? A lot of our tools only need a dictionary and can get one from the header of various...

Taking out mention of the deprecated MQ_DP annotation, corresponds with https://docs.google.com/document/d/1ZdRERavtO1k4v0ppVzJ7gu6PHzSydznhYDmvZUb8qPo/edit?usp=sharing