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tf2 / CNest

Copy Number Methods for Detection and Genome Wide Association Tests
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Known issues #2

Closed smshuai closed 3 years ago

smshuai commented 3 years ago

  1. Dockerfile asked for several .txt files that do not exist. Right now using empty files to build.

    COPY src/index.txt /resources
COPY src/index_tab.txt /resources
COPY src/txt_covered_all_coverage.txt /resources
COPY src/QC_gender_example.txt /resources

  2. To avoid segmentation error at step2

    • BAM file needs to be indexed.
    • index.txt needs matched chromosome names as BAM.
tf2 commented 3 years ago

cool, I've updated the main branch to include blank files - hopefully that solves this issue.

we may want to add an automatic check on the BAM files for the index file at some point...