samclip1
Filter sam file for soft and hard clipped alignments
Usage
samclip --ref
ref.fa
<
in.sam
>
out.sam
Usage
In connection with minimap2
-
minimap2 ref.fa R1.fq R2.fq | samclip --ref ref.fa | samtools sort > out.bam
Overview
Filter SAM file for soft & hard clipped alignments
Options
-
--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)
Releases
Unchanged in 3 releases since Debian 11 (Bullseye).