Specific case of "bedtools intersect"
0
0
Entering edit mode
2.3 years ago
predeus ★ 2.0k

Hi all,

I have a BAM file of an alignment, and I need to remove the reads that are fully contained within certain intervals, provided as a GFF file (could be converted to BED).

I know bedtools intersect has the -v option and supports BAM files; however, running the command like this produces the result that is clearly wrong (I just looked at it in the IGV):

bedtools intersect -v -f 1.0 -a old.bam -b int.bed  > new.bam

Can someone explain how does -f option work here, and what would be a good way to achieve what I'm trying to do?

I can, of course, just do a direct overlap with -wao style, BED-formatted output, then get the list of read names which overlap the intervals by exactly a read length, and then remove the reads from the BAM file by their name list. But this does seem cumbersome.

Thank you, as always.

bedtools BAM • 1.1k views
ADD COMMENT
1
Entering edit mode

On paper, the command you used looks correct to me. -v -f 1 means that you select against old.bam reads fully mapped on int.bed intervals.

What exactly is wrong in IGV ?

ADD REPLY
0
Entering edit mode

Basically wrong reads are removed. You can see which ones overlapped the intervals, and that's not what was removed at all.

ADD REPLY
1
Entering edit mode

Does not answer your question but samtools view has --output-unselected option that might be of use http://www.htslib.org/doc/samtools-view.html

ADD REPLY
0
Entering edit mode

Maybe you can try pybedtools.

ADD REPLY

Login before adding your answer.

Traffic: 1483 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6