Question: Confused By Wgsim Output
0
gravatar for Travis
6.6 years ago by
Travis2.7k
USA
Travis2.7k wrote:

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?

ADD COMMENTlink modified 5.8 years ago • written 6.6 years ago by Travis2.7k
1
gravatar for Pierre Lindenbaum
6.6 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum102k wrote:

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

ADD COMMENTlink written 6.6 years ago by Pierre Lindenbaum102k
0
gravatar for Travis
6.6 years ago by
Travis2.7k
USA
Travis2.7k wrote:

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?

ADD COMMENTlink written 6.6 years ago by Travis2.7k
1

That is correct.

ADD REPLYlink written 6.6 years ago by Nilshomer100

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

ADD REPLYlink written 6.6 years ago by Travis2.7k

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

ADD REPLYlink written 6.5 years ago by lh330k
0
gravatar for Travis
6.6 years ago by
Travis2.7k
USA
Travis2.7k wrote:

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?

ADD COMMENTlink written 6.6 years ago by Travis2.7k

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

ADD REPLYlink written 6.6 years ago by Michael Schubert6.7k

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

ADD REPLYlink written 6.6 years ago by Travis2.7k
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