Remove Soft Clipped Bases

Question

[Clare]

I want to conduct some computations using a python script directly on some BWA aligned bam files, and to do this I need to remove the soft clipped bases. i.e. if the cigar string and read is: 2S8M CCTGGAGAAT I want to clip so it becomes: 8M TGGAGAAT

I tried to do this using clip reads in GaTK but the hardclip option is throwing errors and is unsupported.

Is there anyway to remove the soft clip bases with another piece of software.

Because my coverage is not very high, I don't want to disable softclipping in BWA, as I will loose a lot of coverage.

Thanks

[Devon Ryan]

Can't you just parse the CIGAR string in your script and take care of it there?

Answer 1

[Pierre Lindenbaum]

I just wrote a program removing the clipped bases/qual

see https://github.com/lindenb/jvarkit/wiki/Biostar84452

Example:

$  java -jar dist/biostar84452.jar samtools-0.1.18/examples/toy.sam > out.sam

@HD    VN:1.4    SO:unsorted
@SQ    SN:ref    LN:45
@SQ    SN:ref2    LN:40
@PG    ID:0    PN:com.github.lindenb.jvarkit.tools.biostar.Biostar84452    VN:b5ebf67dd2926d8a6afadb4d1e36a4959508057f    CL:samtools-0.1.18/examples/toy.sam
(...)
r002    0    ref    9    0    2I6M1P1I1P1I4M2I    *    0    0    AAAGATAAGGGATAAA    *
(...)


$ grep r002 samtools-0.1.18/examples/toy.sam
r002    0    ref    9    30    1S2I6M1P1I1P1I4M2I    *    0    0    AAAAGATAAGGGATAAA    *

[Pierre Lindenbaum]

this tool was cited in the suppl. mat. of http://genome.cshlp.org/content/early/2017/10/05/gr.218032.116.full.pdf+html

Answer 2

[opplatek]

bamutils / removeclipping (GitHub) works also very nice.

P.S. I know the post is very old but this might be handy for somebody else reading this post in the future.

[terdon]

I'm afraid your link is broken. Are you referring to https://github.com/statgen/bamUtil? That doesn't seem to have a removeclipping tool.

[opplatek]

I have edited the answer and link should be working now. The team stopped actively supporting the tools and they have migrated here. However, I don't see the clipping utility there. The 'old' one still works, though. The bamUtil is completely different package.