samclip

samclip --ref ref.fa < in.sam > out.sam

In connection with minimap2

minimap2 ref.fa R1.fq R2.fq | samclip --ref ref.fa | samtools sort > out.bam

Filter SAM file for soft & hard clipped alignments

--help

This help

--version

Print version and exit

--ref FASTA

Reference genome - needs FASTA.fai index

--max NUM

Maximum clip length to allow (default=5)

--invert

Output rejected SAM lines and ignore good ones

--debug

Print verbose debug info to stderr

--progress N

Print progress every NUM records (default=100000,none=0)

https://github.com/tseemann/samclip

This manpage was written by Andreas Tille for the Debian distribution and
can be used for any other usage of the program.