table of contents
| DWGSIM:(1) | User Commands | DWGSIM:(1) |
NAME¶
dwgsim: - a short read simulatorSYNOPSIS¶
dwgsim [options] <in.ref.fa> <out.prefix>DESCRIPTION¶
DWGSIM is a short read simulator which simulates reads from modern sequencing platforms.OPTIONS¶
- -e FLOAT
- per base/color/flow error rate of the first read [from 0.020 to 0.020 by 0.000]
- -E FLOAT
- per base/color/flow error rate of the second read [from 0.020 to 0.020 by 0.000]
- -i
- use the inner distance instead of the outer distance for pairs [False]
- -d INT
- outer distance between the two ends for pairs [500]
- -s INT
- standard deviation of the distance for pairs [50.000]
- -N INT
- number of read pairs (-1 to disable) [-1]
- -C FLOAT
- mean coverage across available positions (-1 to disable) [100.00]
- -1 INT
- length of the first read [70]
- -2 INT
- length of the second read [70]
- -r FLOAT
- rate of mutations [0.0010]
- -F FLOAT
- frequency of given mutation to simulate low fequency somatic mutations [0.5000] NB: freqeuncy F refers to the first strand of mutation, therefore mutations on the second strand occour with a frequency of 1-F
- -R FLOAT
- fraction of mutations that are indels [0.10]
- -X FLOAT
- probability an indel is extended [0.30]
- -I INT
- the minimum length indel [1]
- -y FLOAT
- probability of a random DNA read [0.05]
- -n INT
- maximum number of Ns allowed in a given read [0]
- -c INT
- generate reads for [0]: 0: Illumina 1: SOLiD 2: Ion Torrent
- -S INT
- generate reads [0]: 0: default (opposite strand for Illumina, same strand for SOLiD/Ion Torrent) 1: same strand (mate pair) 2: opposite strand (paired end)
- -f STRING
- the flow order for Ion Torrent data [(null)]
- -B
- use a per-base error rate for Ion Torrent data [False]
- -H
- haploid mode [False]
- -z INT
- random seed (-1 uses the current time) [-1]
- -M
- generate a mutations file only [False]
- -m FILE
- the mutations txt file to re-create [not using]
- -b FILE
- the bed-like file set of candidate mutations [(null)]
- -v FILE
- the vcf file set of candidate mutations (use pl tag for strand) [(null)]
- -x FILE
- the bed of regions to cover [not using]
- -P STRING
- a read prefix to prepend to each read name [not using]
- -q STRING
- a fixed base quality to apply (single character) [not using]
- -Q FLOAT
- standard deviation of the base quality scores [2.00]
- -s INT
- standard deviation of the distance for pairs [50.000]
- -h
- print this message
Note: For SOLiD mate pair reads and BFAST, the first read is F3 and the second is R3. For SOLiD mate pair reads and BWA, the reads in the first file are R3 the reads annotated as the first read etc.
Note: The longest supported insertion is 4294967295.
| September 2015 | dwgsim: 0.1.11 |