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12-18-2012, 03:15 AM
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#1 |
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Just a member
Location: Southern EU Join Date: Nov 2012
Posts: 103
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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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12-18-2012, 05:26 AM
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#2 |
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Just a member
Location: Southern EU Join Date: Nov 2012
Posts: 103
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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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