Confused By Wgsim Output

Question

[Travis]

Hi all,

I am generating a million paired end reads with wgsim using the following command

  wgsim -N 1000000 -1 100 -2 100 hg19.fa read1.fq read2.fq

The output files are generated fine. The screen output seems to be some sort of mutation report but I can't seem to spot the correlation between this and the content of my output files.Am I totally misinterpreting something?

Answer 1

[Pierre Lindenbaum]

As far as I remember the output to stdout is a SAM pileup file including the positions of the mutations. http://samtools.sourceforge.net/pileup.shtml

Answer 2

[Travis]

The stdout looks like this

chrX    89985560        T       C       -
chrX    89990640        T       Y       +  
chrX    89991017        C       M       +
chrX    89991096        G       R       +
chrX    89994004        A       R       + 
chrX    89994987        A       W       +
chrX    89995790        A       R       +

Even when I generate 100 reads the stdout is 2,923,254 lines long. So is is just generating and outputting mutations for the whole genome and then generating reads indepently of these across the genome?

[Nilshomer]

That is correct.

[Travis]

nils - can you point me to where I can get a description of the above format ?

[lh3]

The last column gives hom (-) or het (+).

Answer 3

[Travis]

So where do I find out what the 'W's and 'R's etc mean? And also, what is the quickest way of finding out which of these mutations were incorporated into the actual reads I generated?

[Michael Schubert]

Travis, please edit your initial questions or post comments for further clarification/requests. Answers should be used to answer your question. Thanks.

[Travis]

Apologies. Will do in future. Was just trying to increase the visibility of the comment.