samtools-targetcut - cut fosmid regions (for fosmid pool only)

       Written by Heng Li from the Sanger Institute.

       This  command  identifies  target  regions  by  examining  the continuity of read depth, computes haploid
       consensus sequences of targets and outputs a SAM with each  sequence  corresponding  to  a  target.  When
       option  -f  is  in use, BAQ will be applied. This command is only designed for cutting fosmid clones from
       fosmid pool sequencing [Ref. Kitzman et al. (2010)].

       samtools-targetcut - cut fosmid regions (for fosmid pool only)

-QminBaseQ
               Ignore bases with quality less than minBaseQ.

       -iinPenalty
               Penalty for in state transition.

       -0em0  Emission score 0.

       -1em1  Emission score 1.

       -2em2  Emission score 2.

       -fref  Reference FASTA file.

samtools(1)

       Samtools website: <http://www.htslib.org/>

samtools-1.21                                   12 September 2024                          samtools-targetcut(1)

       samtools targetcut [-QminBaseQ] [-iinPenalty] [-0em0] [-1em1] [-2em2] [-fref] in.bam