A Problem About Simulate Colour Reads With Wgwin Tool

Question

[User 0473]

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?

thanks

Answer 1

[Ben Lange]

This may be from the wrong version of wgsim, but I'm not seeing a -c command line argument. https://github.com/lh3/wgsim/blob/master/wgsim.c

fprintf(stderr, "\n");
fprintf(stderr, "Program: wgsim (short read simulator)\n");
fprintf(stderr, "Version: %s\n", PACKAGE_VERSION);
fprintf(stderr, "Contact: Heng Li <[e-mail]>\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");