TCGA WGS samples, Liver cancers

mskcc / tempo

CCS research pipeline to process WES and WGS TN pairs

https://cmotempo.netlify.app/

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Closed evanbiederstedt closed 5 years ago

evanbiederstedt commented 5 years ago

I downloaded some Liver cancers from ICGC

They're here: /juno/work/taylorlab/cmopipeline/viral_WGS_ICGC_bams/Liver_samples

It looks like there are 2 BAMs that are still being converted to paired end FASTQs

These are not done by lane---I downloaded the BAM, sorted by QNAME, and created FASTQs. They are big files.

It's a challenge :motivated_face_emoji: ✊

evanbiederstedt commented 5 years ago

I need to create a *tsv for this

kpjonsson commented 5 years ago

Any update on this? Still relevant?