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.