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Read VCF file that contains more than just the GT field #6

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golharam opened this issue Dec 17, 2020 · 2 comments
Open

Read VCF file that contains more than just the GT field #6

golharam opened this issue Dec 17, 2020 · 2 comments

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@golharam
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My VCFs contain more than just the GT in the sample column, e.g. GT:AD:DP:GQ:PL 1/1:0,3:3:9:89,9,0. This package expects ONLY the GT field to be present. It would be nice for this package to parse the GT field from the other fields.
@jordur
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jordur commented Feb 11, 2022 •
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Hi @golharam. Did you find how to fix it?
I did it with bcftools just as described here.
Regards

@golharam
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Yes, I had to parse out the GT field only.

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@golharam @jordur