Cannot parse ExAC VCF - Githubissues

broadinstitute / oncotator

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Cannot parse ExAC VCF #343

Closed LeeTL1220 closed 8 years ago

LeeTL1220 commented 8 years ago

pyVCF

SyntaxError: One of the INFO lines is malformed: ##INFO=<ID=DP_HIST,Number=R,Type=String,Description="Histogram for DP; Mids: 2.5|7.5|12.5|17.5|22.5|27.5|32.5|37.5|42.5|47.5|52.5|57.5|62.5|67.5|72.5|77.5|82.5|87.5|92.5|97.5">

LeeTL1220 commented 8 years ago

Solved with latest (unreleased master branch as of this writing) version of PyVCF.

https://github.com/jamescasbon/PyVCF

LeeTL1220 commented 8 years ago

[x] Update build venv script
[x] Unit tests all pass
[x] Update Dockerfile
[x] Update pysam version to support ExAC downloaded index.

LeeTL1220 commented 8 years ago

Closed by #344