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Created python to generate IRMA vcf file #304

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merged 21 commits into from
Aug 16, 2024
Merged

Created python to generate IRMA vcf file #304

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5de5254
created python for irma vcf
svarona Aug 1, 2024
c7a3bbe
@saramonzon changes to add minority variants WIP
svarona Aug 1, 2024
5e5475b
Added frequency and depth as parameter filters
svarona Aug 1, 2024
82d7806
Added TOTAL_DP to stats
svarona Aug 1, 2024
4eeb526
Updated VCF data to fit in VCFv4.2 format
svarona Aug 1, 2024
5cf1b58
Exclude reference alles in both alignment and stats files
svarona Aug 1, 2024
349928b
Added code to update minority allele
svarona Aug 1, 2024
0aeca87
Added code for minority deletions
svarona Aug 1, 2024
6cfb704
Fixed line that was excluding deletions
svarona Aug 1, 2024
93f6d0e
Added total dp
svarona Aug 1, 2024
3e3c350
refactored a little bit
svarona Aug 1, 2024
b5c8930
Updated docstrings
svarona Aug 1, 2024
a63f931
black
svarona Aug 1, 2024
2f068ef
Updated changelog
svarona Aug 1, 2024
fcf5efc
Managed deletions at the begining of alignment
svarona Aug 6, 2024
957e7c3
Managed missing data in stats
svarona Aug 6, 2024
e6152b6
Managed minority deletions
svarona Aug 6, 2024
cf33266
managed minority deletions
svarona Aug 6, 2024
a435ca1
black
svarona Aug 6, 2024
23d28c3
Fixed alt_allele in insertions
svarona Aug 7, 2024
1cb2fa2
Added management of low af insertions at the end of the sequence
svarona Aug 7, 2024
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -56,6 +56,7 @@ Code contributions to the new version:
- Updated services.json, mtbseq's lablog, viralrecon's lablog and assembly's config file [#299](https://github.com/BU-ISCIII/buisciii-tools/pull/299)
- Added lablog to automate gene characterization with emmtyper, including unzipping assemblies. [#300](https://github.com/BU-ISCIII/buisciii-tools/pull/300)
- Fixed 99-stats (MAG) template. [#301](https://github.com/BU-ISCIII/buisciii-tools/pull/301)
- Created a python script to process IRMA's results and create a standard vcf file against reference. [#304](https://github.com/BU-ISCIII/buisciii-tools/pull/304)
- Fixed IRMA's lablog so that the sequences of the samples are not displayed several times neither in the .txt files of each influenza type nor in all_samples_completo.txt [#305](https://github.com/BU-ISCIII/buisciii-tools/pull/305)
- Modified bioinfo_doc.py so that new lines in the delivery message are applied in the email [#307](https://github.com/BU-ISCIII/buisciii-tools/pull/307)
- Added several improvements in lablog_viralrecon (created log files, modified check_references function behaviour, enabled config files regeneration) [#306](https://github.com/BU-ISCIII/buisciii-tools/pull/306)
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