Question: samtools sort by something other than position/name?
0
gravatar for anderspitman
18 days ago by
anderspitman30
United States
anderspitman30 wrote:

I'm trying to automatically compare BAM files being output by bowtie2 (for a continuous integration system). Currently using bamUtil diff which works well, except I'm noticing sometimes 2 lines in the BAM file will have the same name/start position, but represent different reads. For whatever reason, bowtie2 sometimes reverses the order of the lines, so bamUtil's algorithm calls a mismatch. I see several potential solutions to this problem:

  1. Get samtools to sort by another dimension in addition to position/name. Pretty much anything should do. Can this be done? I don't see any options in the man page.

  2. Use another comparision tool than bamUtil which doesn't have this problem. Honestly a stand-alone program for diffing would be best for me anyway and I'm considering writing one.

  3. Find some way to get bowtie2 to be more deterministic in its ordering. Any ideas here?

samtools • 178 views
ADD COMMENTlink modified 17 days ago • written 18 days ago by anderspitman30

For whatever reason, bowtie2 sometimes reverses the order of the lines, so bamUtil's algorithm calls a mismatch.

show us an example please.

ADD REPLYlink written 18 days ago by Pierre Lindenbaum103k

I confirmed that bamHash shows the files as matching. I think my solution for now is to just use that. I'm still a little concerned that I don't know which stage of my pipeline is interleaving the reads. From what I've read I should be accounting for all sources of non-determinism (using single core, etc). I might dig deeper into this at some point but after reading up on bamHash and testing it out I think that's what I need. Thanks for the help. If you move your comment suggesting bamHash to an answer I'll accept it.

ADD REPLYlink written 17 days ago by anderspitman30

I've moved my comment to an answer. Please double check, though, that BamHash is really doing the comparison you want and that you don't care about mapping positions being the same (if you just want to ensure the same entries are contained in both files, regardless of whether/how they're mapped then you're good to go with BamHash).

ADD REPLYlink written 17 days ago by Devon Ryan74k
0
gravatar for Devon Ryan
18 days ago by
Devon Ryan74k
Freiburg, Germany
Devon Ryan74k wrote:

Exactly which parts of the alignments do you want to be diffed? If you just care about name/sequence then you can use bamHash. If you want more than that then you'll need a custom solution. There are no options to have samtools sort in a 3rd way (no one has ever needed that).

ADD COMMENTlink written 18 days ago by Devon Ryan74k
0
gravatar for Pierre Lindenbaum
18 days ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum103k wrote:

Get samtools to sort by another dimension in addition to position/name.

easy in java with htsjdk, I've written a program sorting on REF/Name : http://lindenb.github.io/jvarkit/SortSamRefName.html https://github.com/lindenb/jvarkit/blob/master/src/main/java/com/github/lindenb/jvarkit/tools/misc/SortSamRefName.java

Use another comparision tool than bamUtil which doesn't have this problem

search biostars : https://www.google.fr/search?q=compare+bam+site%3Abiostars.org

ADD COMMENTlink written 18 days ago by Pierre Lindenbaum103k
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