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extra 'GT' added to vcf #59

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abelhj opened this issue Mar 23, 2016 · 1 comment
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extra 'GT' added to vcf #59

abelhj opened this issue Mar 23, 2016 · 1 comment

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@abelhj
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abelhj commented Mar 23, 2016

Is there a reason this 'GT' needs to added when len(var_list)<9? It makes things weird with 8 col vcfs.

https://github.com/hall-lab/svtools/blob/master/svtools/vcf/variant.py#L27-L34
@ernfrid
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ernfrid commented Mar 29, 2016

I suspect this was behavior of a specific tool (vcfpaste maybe?) in the original code base. I'll check.

ernfrid added a commit to ernfrid/svtools that referenced this issue Mar 29, 2016
@ernfrid
stop auto-adding GT to the format field on 8-column VCFs. SVTyper adds
d238d20 
this itself and is the only place we think this matters. Closes hall-lab#59.
@ernfrid ernfrid mentioned this issue Mar 29, 2016
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@ernfrid @abelhj