Variant dbsnp rs id tracking in vcf2adam and ADAM2Vcf #1103

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jpdna opened this Issue Aug 7, 2016 · 5 comments

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jpdna commented Aug 7, 2016

Currently when running vcf2adam followed by adam2vcf the ID column in the original VCF file, commonly a dbSNP rs_id, is lost.

Looking at bdg-formats, I now realize that there is no ID field in Variant, and I am not sure where ID would be stored if we wanted to preserve it. One possibility is the attributes field of Variant Annotation. I'd tend to suggest that the ID field is so basic and practically useful to many users that there should be a nullable field for it in Variant. Or am I missing where ID is currently stored?

What do you think @heuermh and @fnothaft ?

@fnothaft fnothaft referenced this issue in bigdatagenomics/bdg-formats Aug 7, 2016

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Add back dbSnp ID field #96

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heuermh Aug 25, 2016

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Fixed by #1131

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heuermh commented Aug 25, 2016

Fixed by #1131

@heuermh heuermh modified the milestone: 0.20.0 Sep 7, 2016

@heuermh heuermh referenced this issue Sep 7, 2016

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Release ADAM version 0.20.0 #1048

47 of 61 tasks complete

@heuermh heuermh modified the milestones: 0.20.0, 0.22.0, 0.21.0 Oct 13, 2016

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fnothaft Nov 8, 2016

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Should be resolved by #1250.

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fnothaft commented Nov 8, 2016

Should be resolved by #1250.

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heuermh Nov 11, 2016

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Actually, this one was fixed earlier than #1250 by #1131 but won't show up on master until #1135 is merged.

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heuermh commented Nov 11, 2016

Actually, this one was fixed earlier than #1250 by #1131 but won't show up on master until #1135 is merged.

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heuermh Nov 16, 2016

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Fixed by #1131.

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heuermh commented Nov 16, 2016

Fixed by #1131.

@heuermh heuermh closed this Nov 16, 2016

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