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.
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