SAMCLIP(1) | User Commands | SAMCLIP(1) |
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¶
AUTHOR¶
This manpage was written by Andreas Tille for the Debian
distribution and
can be used for any other usage of the program.
May 2020 | samclip 0.4.0 |