1samtools-targetcut(1)        Bioinformatics tools        samtools-targetcut(1)
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NAME

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

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

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

22       -Q minBaseQ
23               Ignore bases with quality less than minBaseQ.
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26       -i inPenalty
27               Penalty for in state transition.
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29       -0 em0  Emission score 0.
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31       -1 em1  Emission score 1.
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33       -2 em2  Emission score 2.
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35       -f ref  Reference FASTA file.
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AUTHOR

39       Written by Heng Li from the Sanger Institute.
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SEE ALSO

43       samtools(1)
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45       Samtools website: <http://www.htslib.org/>
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49samtools-1.13                     7 July 2021            samtools-targetcut(1)