Truncating alignments in a SAM/BAM file

Question

[everj]

Hi everyone,

I am interested in narrowing or truncating the alignment of reads in SAM or BAM formatted files by X NTs from each end. My reason is that the detection of indels is a bit muddied by a percentage of reads reaching into or across indels which may be poor alignments even after quality aligned reads trimming and removing clipped reads.

Any suggestions would be appreciated.

Thanks!
John

Answer 1

[GenoMax]

• You can use bamUtils (LINK).
• https://www.nature.com/articles/s41598-017-01703-6
• Also this may work: Trim bam file reads to the same length
• http://www.htslib.org/doc/samtools-ampliconclip.html