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New ivar_variants_to_vcf.py #32

Merged
merged 12 commits into from
Jul 19, 2024
Merged

New ivar_variants_to_vcf.py #32

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0ef6e91
New ivar_variants_to_vcf.py
Shettland May 21, 2024
327d2f4
Updated CHANGELOG.md
Shettland May 21, 2024
13a698c
Fixed ivar_to_vcf deleting close variants after merge
Shettland Jun 6, 2024
bcf3010
Updated ivar-to-vcf, cleaning columns and saving not-merged varints
Shettland Jun 7, 2024
b0d7f27
Updated ivar-to-vcf, linting1
Shettland Jun 7, 2024
98b6896
Re-update of ivar-to-vcf. v2
Shettland Jun 21, 2024
276967f
Small fixes to ivar-vcf_v2 script
Shettland Jun 26, 2024
0abd3d5
Updated CHANGELOG.md
Shettland Jun 26, 2024
430f748
Linting ivar-to-vcf
Shettland Jun 26, 2024
f990ed8
Included reviewer comments
Shettland Jun 27, 2024
62aedf0
Skipped refs when ref_dp is 0
Shettland Jul 1, 2024
8fee2d2
ref AF is now calculated using ref_DP
Shettland Jul 2, 2024
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -26,6 +26,7 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
- [[PR #401](https://github.com/nf-core/viralrecon/pull/401)] - Added option to add a custom annotation
- [[PR #417](https://github.com/nf-core/viralrecon/pull/417)] - Allow skipping of Freyja bootstrapping module & freyja module update
- [[PR #434](https://github.com/nf-core/viralrecon/pull/434)] - Add blast result filtering through `min_contig_length` and `min_perc_contig_aligned`.
- [[PR #]()] - Refactored old ivar_variants_to_vcf.py with new functionalities like a quality threshold.

### Parameters

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