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Old 02-27-2014, 09:24 AM   #23
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Location: los angeles

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


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( and, 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.
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