Soft-clipping of a BAM file based on regions from the BED file

Question

[lechu]

I have a BED file with genomic regions. Is there a tool that, using this BED file, would help me to subset this BAM file so that all reads (and parts of reads) that fall outside of the regions in the BED file would be soft-clipped?

Answer 1

[Pierre Lindenbaum]

tool for bam soft clipping reads within bed file regions

Limiting variant calls to amplicon target regions?

paired-end bam clip bases outside insert range

[lechu]

This truly gives impression I'm a a lazy tard that can't use google ;). Thanks!

[GenoMax]

@Pierre has answers/code written for questions that have not even been asked. These were examples where he already provided answers. So don't feel bad :-)

[lechu]

I looked at the PcrClipReads tool developed by @Pierre. It's great, but as far as I understand, it does not handle cases of reads that overlap two (or more) regions. I realized I was not precise in my question. In a situation like the one depicted below I would only like to clip bases marked x (read 1 should not be clipped). The goal is to use exonic regions and remove everything the protrudes outside of exonic ranges (this may require "internal' clips in the reads). Equally good alternative would be to somehow reset the qualities of the bases to be clipped to zero (instead of clipping). I tried to do it using sam2tsv (also from @Pierre), but ended up with file sizes that were impossible to handle (I need it for whole transcriptome data). Then I run out of ideas.

        ----------           ---  read 1 (goes across two exons)
        ----------xxx        ---  read 2 (goes across two exons, some mapped to intron)
        ----------xxx             read 3 (mapped to single regions + some protrusion)
       |-REGION1-|           |-REGION2-|

[Pierre Lindenbaum]

update 2021: there is now samtools ampliconclip samtools-ampliconclip http://www.htslib.org/doc/samtools-ampliconclip.html

Clip reads in a SAM compatible file based on data from a BED file.