View Single Post
Old 02-27-2014, 09:24 AM   #23
coco90417
Junior Member
 
Location: los angeles

Join Date: Feb 2014
Posts: 1
Default Varscan vcf output for indel

Hi,

I am also encountering issues with vcf output of indels. I have got indels that look like this:

1 984171 . CAG AG .
1 1588744 . AGCG GCG .

I checked genome browser for the context of both mutations(http://genome.ucsc.edu/cgi-bin/hgTra...A984170-984180 and http://genome.ucsc.edu/cgi-bin/hgTra...588740-1588750), it seems that the first one is supposed to be simple deletion of the first base and the should look like this:

1 984170 . GC G .

And the second one can be either represented by a block substitution that looks like this:

1 1588743 . AAG AG .

or a deletion (if you align the deletion to the left) that looks like this:

1 1588742 . GA G .

So I do not know whether I did something wrong or it was because Varscan has a different vcf output format for indels?

Please help me. Many many thanks.
coco90417 is offline   Reply With Quote