NAME
samclip - filter SAM file for soft and hard clipped alignments
SYNOPSIS
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
DESCRIPTION
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)
SEE ALSO
-
https://github.com/tseemann/samclip
AUTHOR
This manpage was written by Andreas Tille for the Debian distribution and
can be used for any other usage of the program.