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Old 12-18-2012, 03:15 AM   #1
syfo
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Default BEDtools intersect output is BED instead of BAM

Hi all,
I want to discard the reads that overlap some blacklist regions, so I use
intersectbed -abam -v -a readfile.bam -b badregions.bed

I get 9 entries in BED format, despite the abam option ("The A input file is in BAM format. Output will be BAM as well.")

Now if I add the -wa option I get 3.5M entries, again in BED format.

Any idea about what is going on?
thanks
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Old 12-18-2012, 05:26 AM   #2
syfo
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OK, the command line was wrong; it should have been
intersectbed -v -abam readfile.bam -b badregions.bed
problem solved
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