converting a bam to bed file

Question

[erl1977]

Hi all, I have a bam file that has many supplemental alignments within it (the XA tag). These are single-end reads that were mapped with a bwa all/samse pipeline. I'm trying to convert the bam file to a bed file in which each supplemental mapping is also printed out to the bed file as a unique line. So, for example, I have a file with a entry of:

SEQ_20  0       chr1    184669033       0       16M     *       0       0       AAAAAAAAAAAAACAT        IIIIIIIIIIIIIIII        XT:A:R  NM:i:0  X0:i:3274       XM:i:0  XO:i:0  XG:i:0  MD:Z:16 XA:Z:chr3,-59868032

I'm using bedtools bamtobed and get this:

chr1    184669032       184669048       SEQ_20  0       +

But, I'm trying to also have it print out the secondary alignment from the XA tag to get something like:

chr1    184669032       184669048       SEQ_20  0       +
chr3    59868032       59868048       SEQ_20  0       1

I can't seem to find a good way of doing this, and I haven't been able to find a program to do it.

Thanks

Answer 1

[Pierre Lindenbaum]

using bioalcidaejdk: http://lindenb.github.io/jvarkit/BioAlcidaeJdk.html

java -jar ${JVARKIT_DIST}/bioalcidaejdk.jar  -e 'stream().filter(R->!R.getReadUnmappedFlag()).forEach(R->{println(R.getContig()+"\t"+(R.getStart()-1)+"\t"+R.getEnd()+"\t"+R.getReadName()+"\t"+R.getMappingQuality()+"\t"+(R. getReadNegativeStrandFlag()?"-":"+"));for(SAMRecord R2: htsjdk.samtools.SAMUtils.getOtherCanonicalAlignments(R)){println(R2.getContig()+"\t"+(R2.getStart()-1)+"\t"+R2.getEnd()+"\t"+R2.getReadName()+"\t"+R2.getMappingQuality()+"\t"+(R2.getReadNegativeStrandFlag()?"-":"+"));} });' in.bam

[erl1977]

Thanks for this. I tried it, but it gives the same output as bedtools bamtobed. I'm going to try playing around with it, see if I can get it to work

[Pierre Lindenbaum]

Thanks for this. I tried it, but it gives the same output as bedtools bamtobed

I think it's because your bam uses the old XA attribute. (not 'SA')

https://samtools.github.io/hts-specs/SAMtags.pdf

SA Z Other canonical alignments in a chimeric alignment

[erl1977]

I tried manually changing the XA tag to SA, but still didn't work. I'll try to figure something out manually or remap with another program. Thanks for your help