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Use HaplotypeCaller #2

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trickytank opened this issue Aug 1, 2022 · 2 comments
Open

Use HaplotypeCaller #2

trickytank opened this issue Aug 1, 2022 · 2 comments
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Use GATK HaplotypeCaller
@trickytank trickytank self-assigned this Aug 8, 2022
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Seems to work, but now have to document.

@igarcia17
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igarcia17 commented Apr 5, 2024 •
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Dear @bahlolab and @trickytank

We are trying to use vcf2likdatagen.pl to get brlmm files from our vcf files. These files were produced by GATK HaplotypeCaller. In the documentation that you provide in this repository (https://github.com/bahlolab/linkdatagen-manual) it seems that it can be an option to the argument --vc, but unfortunately I am unable to find the updated script.

How can we run it for this type of data?

Kind regards and thank you in advance for your support
Ines

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@trickytank @igarcia17