Question: A Problem About Simulate Colour Reads With Wgwin Tool
gravatar for User 0473
8.8 years ago by
User 04730
User 04730 wrote:

I use wgsim with -c parameter to simulate solid reads. Why does it always produce base reads?

could anyone help me to resolve this problem?


simulation solid • 1.6k views
ADD COMMENTlink modified 5.8 years ago by Biostar ♦♦ 20 • written 8.8 years ago by User 04730
gravatar for Ben Lange
8.5 years ago by
Ben Lange190
Minneapolis, MN
Ben Lange190 wrote:

This may be from the wrong version of wgsim, but I'm not seeing a -c command line argument.

fprintf(stderr, "\n");
fprintf(stderr, "Program: wgsim (short read simulator)\n");
fprintf(stderr, "Version: %s\n", PACKAGE_VERSION);
fprintf(stderr, "Contact: Heng Li <>\n\n");
fprintf(stderr, "Usage:   wgsim [options] <in.ref.fa> <out.read1.fq> <out.read2.fq>\n\n");
fprintf(stderr, "Options: -e FLOAT      base error rate [%.3f]\n", ERR_RATE);
fprintf(stderr, "         -d INT        outer distance between the two ends [500]\n");
fprintf(stderr, "         -s INT        standard deviation [50]\n");
fprintf(stderr, "         -N INT        number of read pairs [1000000]\n");
fprintf(stderr, "         -1 INT        length of the first read [70]\n");
fprintf(stderr, "         -2 INT        length of the second read [70]\n");
fprintf(stderr, "         -r FLOAT      rate of mutations [%.4f]\n", MUT_RATE);
fprintf(stderr, "         -R FLOAT      fraction of indels [%.2f]\n", INDEL_FRAC);
fprintf(stderr, "         -X FLOAT      probability an indel is extended [%.2f]\n", INDEL_EXTEND);
fprintf(stderr, "         -S INT        seed for random generator [-1]\n");
fprintf(stderr, "         -h            haplotype mode\n");
ADD COMMENTlink modified 12 days ago by RamRS24k • written 8.5 years ago by Ben Lange190
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