1samtools-targetcut(1) Bioinformatics tools samtools-targetcut(1)
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6 samtools targetcut - cut fosmid regions (for fosmid pool only)
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9 samtools targetcut [-Q minBaseQ] [-i inPenalty] [-0 em0] [-1 em1] [-2
10 em2] [-f ref] in.bam
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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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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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39 Written by Heng Li from the Sanger Institute.
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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)