Question: How to remove soft clipping reads
gravatar for Juan Ledesma
9 months ago by
United Kingdom
Juan Ledesma0 wrote:


Does anyone know a way or a tool to remove soft and hard clipping reads from the sam file using Galaxy?


sam samtools • 491 views
ADD COMMENTlink modified 3 months ago by torsten.seemann0 • written 9 months ago by Juan Ledesma0
gravatar for Jennifer Hillman Jackson
9 months ago by
United States
Jennifer Hillman Jackson25k wrote:


Please see the tool NGS: Picard > CleanSam.

Thanks! Jen, Galaxy team

ADD COMMENTlink written 9 months ago by Jennifer Hillman Jackson25k
gravatar for torsten.seemann
3 months ago by
torsten.seemann0 wrote:

Picard CleanSam does not actually remove any reads from the SAM file.

Here is what it does: "Cleans the provided SAM/BAM, soft-clipping beyond-end-of-reference alignments and setting MAPQ to 0 for unmapped reads"

All it does it ADD soft clips to reads that go over the edge accidently.

I have tested this and it seems to be true. No reads are removed.

ADD COMMENTlink written 3 months ago by torsten.seemann0
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