wgsim output

[efoss]

I'm using wgsim to simulate reads. I get reasonable .fq files back, but wgsim also generates output like this:

chr1 11086 G K +
chr1 11353 T W +
chr1 12163 A R +
chr1 12834 T W +
chr1 13036 T K +
chr1 13948 C Y +
chr1 14051 T C -
chr1 14334 G T -
chr1 17241 C T -
chr1 17253 T W +

I'm confused by this. What does this mean?

Thank you.

Eric

[nilshomer]

These are the mutations that are introduced into the genome.
Col1: chromosome
Col2: position
Col3: original base
Col4: new base (IUPAC codes indicate heterozygous)
Col5: which genomic copy/haplotype

[efoss]

I see - it's the IUPAC thing that threw me. Thanks very much for clearing this up.

Eric

[pmaugeri]

Is there a way to export/convert the wgsim output to a VCF file?
Thanks