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epi2me-labs / wf-somatic-variation

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Can input be CRAM #6

Closed kiranpatil222 closed 10 months ago

kiranpatil222 commented 10 months ago

Ask away!

Hi,

Does this Wf take CRAM input , as i wanted to try pipeline woth your ONT aws data, i see CRAM files are available,

Which folder files should one download from the below for Tumor/normal as Pair for analysis

 aws s3 ls --no-sign-request s3://ont-open-data/colo829_2023.04/COLO829/
                           PRE PAK76302/
                           PRE PAO29420/
                           PRE PAO32033/
aws s3 ls --no-sign-request s3://ont-open-data/colo829_2023.04/COLO829BL/
                           PRE PAK76487/
                           PRE PAO33946/
RenzoTale88 commented 10 months ago

Hi @kiranpatil222 the workflow should accept CRAM as an input. The cells used in the blog post are the ones named PAOXXXXX. Keep in mind that the workflow accepts one input bam/cram for tumor and one for normal, and you need to combine multiple cram/bam for the same sample beforehand.