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)].
Ignore bases with quality less than minBaseQ.
Penalty for in state transition.
Emission score 0.
Emission score 1.
Emission score 2.
Reference FASTA file.
Written by Heng Li from the Sanger Institute.
Samtools website: <http://www.htslib.org/>
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