GD2VCF incorrectly reports AMP

barricklab / breseq

breseq is a computational pipeline for finding mutations relative to a reference sequence in short-read DNA resequencing data. It is intended for haploid microbial genomes (<20 Mb). breseq is a command line tool implemented in C++ and R.

http://barricklab.org/breseq

GNU General Public License v2.0

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GD2VCF incorrectly reports AMP #75

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago

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 commented 9 years ago

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 commented 9 years ago

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

Changed state: Fixed

GoogleCodeExporter commented 9 years ago

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