samclip - filter SAM file for soft and hard clipped alignments

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

samclip 0.4.0                                       May 2020                                          SAMCLIP(1)

       Filter SAM file for soft & hard clipped alignments

       samclip - filter SAM file for soft and 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

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

       In connection with minimap2

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