samtools targetcut [-Q minBaseQ] [-i inPenalty] [-0 em0] [-1 em1] [-2 em2] [-f ref] in.bam
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)].
- -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.
Written by Heng Li from the Sanger Institute.
Samtools website: <http://www.htslib.org/>