Planned Data Release: v6

[jharenza]

File(s)

What data file(s) does this issue pertain to?

Release

v6
What release are you using?

Link to OpenPBTA-manuscript

Put a link to the relevant section of the OpenPBTA manuscript here.

Question/issue

Put your question or report your issue here.
This will include updates to:

• Lancet and Vardict files (WXS to be added; vardict file to be fixed) Related to: Where are the WXS samples in the Lancet dataset? #145 and Issues reading in VarDict file #135
• Clinical file (duplicate WGS record in clinical file #131); Add missing sample_id, aliquot_id, RNA tumor_descriptor (Incomplete metadata for RNA-seq biospecimens #156)
• New strelka2 maf (Strelka2 maf file read counts seem incorrect #153)
• Dropping LUMPY (comment)
• New CN seg files from updated benchmarked runs, to include gain/loss info, p-values for Proposed Analysis: Copy number consensus calls #128
• Manta file (Missing sample in pbta-sv-manta.tsv #157)

[jaclyn-taroni]

Is it possible to perform somatic filtering on the LUMPY file as part of the next release? See #27 (comment) from @gonzolgarcia

[jharenza]

@jaclyn-taroni - looking into this - looks like we have to run SVTyper on the VCFs first, then do the specific filtering mentioned in the issue (not sure how standard practice this filtering is). Perhaps this should also be done on Manta to be consistent, but they also seem to have their own filtering as the file is so much smaller (75MB v. 2.7GB). We will have to do some research into these pipelines before we implement so this may need to come in a later release. Will also followup on this comment and ask for suggestions.

[jashapiro]

Hoping this release can also address the strelka2 file issue identified in #153
There was a bug in vcf2maf, that has been fixed in the latest version, 1.6.17.
see: mskcc/vcf2maf#215
https://github.com/mskcc/vcf2maf/releases/tag/v1.6.17

[jaclyn-taroni]

Closed via #190