dwgsim to simulate Illumina reads

[gene coder]

Hello, I want to use dwgsim to simulate Illumina reads from the 1000 Genomes Project. I am particularly interested in individual NA12878.

Does anybody know what settings are (approximately or exactly) correct when it comes to the flags -e, -E, -r -R, -X and -Y (http://sourceforge.net/apps/mediawik...ome_Simulation)? Do you know where I can find technical details (does Illumina publish that?) so I can guess myself.

Can anybody explain those flags to a novice? Sequencing is not my domain.

[nilshomer]

Do you have someone who has an Illumina machine that you could ask for typical settings for -e and -E (base error rate)? For human, the rate of mutation (SNPs) is 1/1000, while for indels it is ~1/10000.

If you are using this tool, sequencing is your domain. -e/-E are the per base mean error rate, -r is the rate of mutation, -R is the fraction of mutations that are indels, and -X controls the indel length distribution (probability of extending an indel).