GD2VCF incorrectly reports AMP

[GoogleCodeExporter]

Using the data from 10.1038/nature11514, specifically the gd file for ZDB172
gdtools GD2GVF -r REL606.gbk ZDB172.gd

The following mutation of the gd file:
AMP     162     28      REL606  12452   3       2       edit=1

Is converted in VCF like this:
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO
REL606  12452   .       AAC             .       .       AF=1.0000

I was expecting it to be something like:
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO
REL606  12452   .       AAC     AACAAC        .       .       AF=1.0000

breseq 0.24rc6 on ubunutu/Linux

Thanks for your help
Marco

Original issue reported on code.google.com by galactus...@gmail.com on 30 Jun 2014 at 1:17

[GoogleCodeExporter]

Thanks for catching that!

It should be fixed in the current version (0.24rc7) that you can download via 
the link here:

http://barricklab.org/breseq

Let me know if you find any other problems with the VCF output.

Original comment by jeffrey....@gmail.com on 30 Jun 2014 at 11:20

[GoogleCodeExporter]

Original comment by jeffrey....@gmail.com on 30 Jun 2014 at 11:20

• Changed state: Fixed

[GoogleCodeExporter]

Thanks for fixing that: I can confirm oyu that this error has been fixed.

Marco

Original comment by galactus...@gmail.com on 2 Jul 2014 at 3:00