Any thoughts on how to access gt_bases in case there is * genotype (deletion spanning variant)?

[everestial]

The vcf 4.3 version introduced a new method of representing a deletion spanning variant by *. We obviously don't want gt_bases output as A/* or as */* but the real variant allele_bases for each sample. Any thoughts on how we can get the real variant allele (i.e gt_bases) in such cases.

See details: http://gatkforums.broadinstitute.org/gatk/discussion/6926/spanning-or-overlapping-deletions-allele https://samtools.github.io/hts-specs/VCFv4.3.pdf

[jamescasbon]

Someone needs to add the 4.3 support. I would start by adding a test case with the new features and then unit testing each one.

PRs welcome!

On 5 June 2017 at 15:49, everestial [email protected] wrote:

The vcf 4.3 version introduced a new method of representing a deletion spanning variant by *. Any thoughts on how we can get the real variant allele (i.e gt_bases) in such cases.

See details: http://gatkforums.broadinstitute.org/gatk/discussion/6926/spanning-or- overlapping-deletions-allele https://samtools.github.io/hts-specs/VCFv4.3.pdf

We obviously don't want gt_bases output as A/* or / but the real variant allele_bases for each sample.

Any thoughts?

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[everestial]

@jamescasbon @martijnvermaat @ian1roberts : Any update on this issue ?

[everestial]

@jamescasbon @martijnvermaat @ian1roberts : Hi there, Have you found any fix on this issue so far?