DWGSIM:

NAME

dwgsim: - a short read simulator

SYNOPSIS

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 occur 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.