hammerlab/filter-bam

Name: filter-bam

Owner: Hammer Lab

Description: Stand-alone utility for filtering a BAM file to specific genomic regions, using Apache Spark.

Created: 2016-11-21 21:25:16.0

Updated: 2016-11-30 20:10:12.0

Pushed: 2016-12-08 16:35:35.0

Homepage: null

Size: 28

Language: Scala

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README

filter-bam

Stand-alone utility for filtering a BAM file to specific genomic regions, using Apache Spark.

Usage

assembly
k-submit \
properties-file <spark properties file> \
rget/scala-2.11/filter-bam-assembly-1.0.0-SNAPSHOT.jar \
.bam \
egions> \
t.bam \
c] [--include-unmapped-mates]

Parameters

• <regions>: comma-separated list of genomic regions, in the format accepted by hammerlab/genomic-loci.
• -c/--count: print the number of reads output, in addition to writing out.bam.
• --include-unmapped-mates: include unmapped reads whose mate-contig and mate-start are set to a value that overlaps <regions>.