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.