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Update igenomes sections and final polish of docs #673

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merged 10 commits into from
Jul 20, 2022
Merged

Update igenomes sections and final polish of docs #673

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a3c473c
update username [skip actions]
FriederikeHanssen Jul 20, 2022
b734c5b
remove addressed todo strings
FriederikeHanssen Jul 20, 2022
caeb83a
add gavin to contirbutors list
FriederikeHanssen Jul 20, 2022
c1c854b
Merge remote-tracking branch 'upstream/dev' into docs_igenomes
FriederikeHanssen Jul 20, 2022
30b4314
add joint germline docs
FriederikeHanssen Jul 20, 2022
c30f8fb
where do the ref genomes come from
FriederikeHanssen Jul 20, 2022
702f3f5
remove duplicated sections
FriederikeHanssen Jul 20, 2022
c82a971
Update docs/usage.md
FriederikeHanssen Jul 20, 2022
395651d
Merge remote-tracking branch 'upstream/dev' into docs_igenomes
FriederikeHanssen Jul 20, 2022
0bc9403
remove duplicated sections
FriederikeHanssen Jul 20, 2022
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3 changes: 2 additions & 1 deletion README.md
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Expand Up @@ -97,7 +97,8 @@ We thank the following people for their extensive assistance in the development
- [Anders Sune Pedersen](https://github.com/asp8200)
- [Chela James](https://github.com/chelauk)
- [David Mas-Ponte](https://github.com/davidmasp)
- [Francesco L](https://github.com/nibscles)
- [Francesco Lescai](https://github.com/lescai)
- [Gavin Mackenzie](https://github.com/GCJMackenzie)
- [Gisela Gabernet](https://github.com/ggabernet)
- [Harshil Patel](https://github.com/drpatelh)
- [James A. Fellows Yates](https://github.com/jfy133)
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7 changes: 6 additions & 1 deletion docs/output.md
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Expand Up @@ -323,7 +323,12 @@ If the haplotype-called VCF files are not filtered, then Sarek should be run wit

**Output directory: `{outdir}/variantcalling/haplotypecaller/<sample>/`**

_TODO_
- `joint_germline.vcf.gz` and `joint_germline.vcf.gz.tbi`
- VCF with tabix index
- `joint_germline_recalibrated.vcf.gz` and `joint_germline_recalibrated.vcf.gz.tbi`
- variant recalibrated VCF with tabix index

</details>

#### GATK Mutect2

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