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mskcc / tempo

CCS research pipeline to process WES and WGS TN pairs
https://cmotempo.netlify.com/
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Manhattan: Tasks needed to complete before CCS "minor" handoff #270

Closed allanbolipata closed 5 years ago

allanbolipata commented 5 years ago

Tasks needed prior to CCS handoff

Tasks needed to complete before Manhattan pipeline gets handed off for testing and CCS runs

268 Implementing GetBaseCountsMultipSample

138/#215 LOHHLA implementation

98/#187 Mutational signatures

We also need to update documentation.

Other tasks needed for first major release

Tasks that are pending but should make the final pipeline

269 germline mutation calls postprocessing

189 NetMHCpan

289 FACETS MAF annotation

If anything is missing, please add here.

kpjonsson commented 5 years ago

I would add #289.

evanbiederstedt commented 5 years ago

Other tasks needed for first major release

I would mention that I think Barry would say his spec's on the slides are probably what he would consider "a first release". From slide p. 4, TaylorBS-nextgen-pipe.pdf

• Comprehensive QC metrics and plots • Final aligned and recalibrated BAM files and indices • FACETS output (purity and high-sensitivity runs with accompanying counts, fits, outputs) • Full annotated, tagged, filtered MAF with integrated clonality and zygosity including whitelists and blacklists, pool of CMO/DMP sequenced normals, etc. • VCF of germline calls with annotated zygosity • MSIsensor score • Mutational signature decomposition • Structural rearrangements • Viral sequence • CH status • HLA genotypes • HLA LOH • Neoantigen binding predictions*

It's largely a judgement call for us what the "first release is".

evanbiederstedt commented 5 years ago

Oppenheimer added stuff; this issue feels now outdated