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Variant calling with short read data #46

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priyanka-surana opened this issue Jun 27, 2023 · 3 comments
Open

Variant calling with short read data #46

priyanka-surana opened this issue Jun 27, 2023 · 3 comments
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feature Requests for new features question Further information is requested user request Requests made by users and public

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@priyanka-surana
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priyanka-surana commented Jun 27, 2023 •
edited by muffato
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Description of feature

Variant calling for short read data. Tools considered: FreeBayes, GATK, samtools mpileup
@priyanka-surana priyanka-surana added enhancement Improvement of the existing features user request Requests made by users and public labels Jun 27, 2023
@priyanka-surana priyanka-surana changed the title Variant calling for short read data Variant calling with short read data Jun 27, 2023
@muffato
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muffato commented Dec 11, 2023

After talking to the Cardiff team, who analysed otter resequencing data, we should go with GATK, which has a standard and complete pipeline (incl. joint-calling) – and investigate nf-core/sarek, which should be doing a lot of that.

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muffato commented Dec 11, 2023

After talking to the HumGen informatics team, it seems sarek can't do per-individual variant calling and joint-calling in the same run. It has to be run twice. They're working on a fork that could do that in the same pipeline run.

@muffato muffato removed the enhancement Improvement of the existing features label Jun 1, 2024
@muffato muffato moved this to To do in variantcalling Jun 5, 2024
@muffato muffato moved this from To do to Triage in variantcalling Jun 10, 2024
@muffato muffato moved this from Todo to Triage in Genome After Party Jun 10, 2024
@muffato muffato added question Further information is requested feature Requests for new features labels Jun 10, 2024
@muffato muffato moved this from Triage to Blocked in variantcalling Jun 13, 2024
@muffato muffato removed the user request Requests made by users and public label Jun 17, 2024
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muffato commented Jun 17, 2024

Waiting for the outcome of #79

@muffato muffato moved this from Todo to Blocked in Genome After Party Jun 18, 2024
@muffato muffato added the user request Requests made by users and public label Jun 26, 2024
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feature Requests for new features question Further information is requested user request Requests made by users and public
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Genome After Party
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variantcalling
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