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Intersection of VCF-files #809

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Tracked by #878
asp8200 opened this issue Nov 4, 2022 · 3 comments
Open
Tracked by #878

Intersection of VCF-files #809

asp8200 opened this issue Nov 4, 2022 · 3 comments
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enhancement New feature or request

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@asp8200
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asp8200 commented Nov 4, 2022

Description of feature

Some users requested that Sarek produce a VCF-file which is the "intersection" of the VCF-files from the different variant-callers. Additional description can be found here:

https://nfcore.slack.com/archives/CGFUX04HZ/p1667579492003829

@adamrtalbot and @drpatelh suggest using bcftools isec for this.

This is somewhat similar to the following issue which we plan to solve using bcftools concat: #738

@asp8200 asp8200 added the enhancement New feature or request label Nov 4, 2022
@FriederikeHanssen
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worked on in PR #792

@asp8200
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asp8200 commented Nov 8, 2022

worked on in PR #792

@FriederikeHanssen : Well, I'm not sure about that 🤔 In #792 I'm using bfctools concat and in this issue #809 we want to use bcftools isec, but first solving #792 should make it easier to solve #809 which is a very similar issue.

@FriederikeHanssen
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Ah my bad I thought the two are in the same PR. Then maybe jus un-assign yourself 🙂

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