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Invoking tabix and bgzip #198

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adamnovak opened this issue Oct 18, 2016 · 0 comments
Open

Invoking tabix and bgzip #198

adamnovak opened this issue Oct 18, 2016 · 0 comments

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@adamnovak
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The tabix and bgzip tools are both important utilities for indexing VCF files. They are part of Samtools, but it looks like the Samtools Dockerfiles only expose samtools itself, and don't let you get at the other binaries.

What's the right way to invoke tabix or bgzip when your pipeline gets its samtools dependency through cgl-docker-lib?

It looks like @heuermh and @jvivian might know the answer, since they Dockerized the different samtools versions.

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