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mskcc / cwl-commandlinetools

Central location for CWL CommandLineTools
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Containerize and write CWL for GATK 3.8 FindCoveredIntervals #34

Closed rhshah closed 5 years ago

rhshah commented 5 years ago

Tool: GATK3.8 FindCoveredIntervals

Location: https://software.broadinstitute.org/gatk/ Version: 3.8-1-0-gf15c1c3ef

rhshah commented 5 years ago

Let us switch to bedtools, as I would like to use it directly instead of the need to use FindCoveredIntervals and then use list2bed.

Let me know your thoughts @ionox0 @shalabhsuman @allanbolipata

This will be the bedtools command: bedtools genomecov -bg -ibam /path/to/bam | bedtools merge -i - > out.bed

or it can be: bedtools genomecov -bg -ibam /path/to/bam > out.bedgraph bedtools merge -i out.bedgraph > out.bed

https://github.com/common-workflow-language/workflows/blob/master/tools/bedtools-genomecov.cwl https://hub.docker.com/r/biocontainers/bedtools/dockerfile