Annotate mapping entries of a BAM file based on overlaps with BED files using BEDtools

tagBam -i run.bam -files RefSeq.bed -names -tag GA > run.tagged.bam

A SAM-tag called GA (GA:Z:XXX) will be added to all entries overlapping with an annotated gene, naming the genes ID.

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Last updated on May 06, 2013