Mercurial > repos > rliterman > csp2
annotate CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/share/man/man1/wgsim.1 @ 68:5028fdace37b
planemo upload commit 2e9511a184a1ca667c7be0c6321a36dc4e3d116d
| author | jpayne |
|---|---|
| date | Tue, 18 Mar 2025 16:23:26 -0400 |
| parents | |
| children |
| rev | line source |
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| jpayne@68 | 1 .TH wgsim 1 "21 June 2017" "samtools-1.5" "Bioinformatics tools" |
| jpayne@68 | 2 .SH NAME |
| jpayne@68 | 3 wgsim \- Whole-genome sequencing read simulator |
| jpayne@68 | 4 .SH SYNOPSIS |
| jpayne@68 | 5 .B wgsim |
| jpayne@68 | 6 [\fI\,options\/\fR] \fI\,<in.ref.fa> <out.read1.fq> <out.read2.fq>\/\fR |
| jpayne@68 | 7 .PP |
| jpayne@68 | 8 <in.ref.fa> must be a fasta file containing a reference genome. |
| jpayne@68 | 9 .PP |
| jpayne@68 | 10 <out.read1.fq> and <out.read2.fq> are the first and second read output files. |
| jpayne@68 | 11 .SH OPTIONS |
| jpayne@68 | 12 .TP |
| jpayne@68 | 13 \fB\-e\fR FLOAT |
| jpayne@68 | 14 base error rate [0.000] |
| jpayne@68 | 15 .TP |
| jpayne@68 | 16 \fB\-d\fR INT |
| jpayne@68 | 17 outer distance between the two ends [500] |
| jpayne@68 | 18 .TP |
| jpayne@68 | 19 \fB\-s\fR INT |
| jpayne@68 | 20 standard deviation [50] |
| jpayne@68 | 21 .TP |
| jpayne@68 | 22 \fB\-N\fR INT |
| jpayne@68 | 23 number of read pairs [1000000] |
| jpayne@68 | 24 .TP |
| jpayne@68 | 25 \fB\-1\fR INT |
| jpayne@68 | 26 length of the first read [70] |
| jpayne@68 | 27 .TP |
| jpayne@68 | 28 \fB\-2\fR INT |
| jpayne@68 | 29 length of the second read [70] |
| jpayne@68 | 30 .TP |
| jpayne@68 | 31 \fB\-r\fR FLOAT |
| jpayne@68 | 32 rate of mutations [0.0010] |
| jpayne@68 | 33 .TP |
| jpayne@68 | 34 \fB\-R\fR FLOAT |
| jpayne@68 | 35 fraction of indels [0.15] |
| jpayne@68 | 36 .TP |
| jpayne@68 | 37 \fB\-X\fR FLOAT |
| jpayne@68 | 38 probability an indel is extended [0.30] |
| jpayne@68 | 39 .TP |
| jpayne@68 | 40 \fB\-S\fR INT |
| jpayne@68 | 41 seed for random generator [\-1] |
| jpayne@68 | 42 .TP |
| jpayne@68 | 43 \fB\-A\fR FLOAT |
| jpayne@68 | 44 discard if the fraction of ambiguous bases higher than FLOAT [0.05] |
| jpayne@68 | 45 .TP |
| jpayne@68 | 46 \fB\-h\fR |
| jpayne@68 | 47 haplotype mode |
| jpayne@68 | 48 .TP |
| jpayne@68 | 49 Parameter defaults are given in square brackets. |
| jpayne@68 | 50 .SH AUTHOR |
| jpayne@68 | 51 Copyright 2008 Genome Research Limited. |
| jpayne@68 | 52 .br |
| jpayne@68 | 53 Copyright 2011 Heng Li. |
| jpayne@68 | 54 .TP |
| jpayne@68 | 55 wgsim is part of samtools, https://github.com/samtools/samtools |