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samtools-targetcut(1) Bioinformatics tools samtools-targetcut(1) 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/> samtools-1.23.1 18 March 2026 samtools-targetcut(1)
NAME | SYNOPSIS | DESCRIPTION | OPTIONS | AUTHOR | SEE ALSO
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