Closed rhshah closed 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
Tool: GATK3.8 FindCoveredIntervals
Location: https://software.broadinstitute.org/gatk/ Version: 3.8-1-0-gf15c1c3ef