NAME

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

SYNOPSIS

       samtools targetcut [-Q minBaseQ] [-i inPenalty] [-0 em0] [-1 em1] [-2 em2] [-f ref] in.bam

DESCRIPTION

       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)].

OPTIONS

       -Q minBaseQ
               Ignore bases with quality less than minBaseQ.

       -i inPenalty
               Penalty for in state transition.

       -0 em0  Emission score 0.

       -1 em1  Emission score 1.

       -2 em2  Emission score 2.

       -f ref  Reference FASTA file.

AUTHOR

       Written by Heng Li from the Sanger Institute.

SEE ALSO

       samtools(1)

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