Provided by: dwgsim_0.1.11-3_amd64
dwgsim: - a short read simulator
dwgsim [options] <in.ref.fa> <out.prefix>
DWGSIM is a short read simulator which simulates reads from modern sequencing platforms.
-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  -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  -2 INT length of the second read  -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  -y FLOAT probability of a random DNA read [0.05] -n INT maximum number of Ns allowed in a given read  -c INT generate reads for : 0: Illumina 1: SOLiD 2: Ion Torrent -S INT generate reads : 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.