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Pull requests: griffithlab/VAtools

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Pull requests list

Allow vep annotation reporter to provide a list of preferred transcripts
#81 by susannasiebert was merged Mar 4, 2025 Loading…
Refactor vcf-expression-annotator to be faster
#79 by susannasiebert was merged Mar 4, 2025 Loading…
Update ref transcript mismatch reporter to handle protein coding variants
#75 by susannasiebert was merged Feb 5, 2024 Loading…
1
Add per-strand allele counts when running vcf-readcount-annotator
#72 by susannasiebert was merged Oct 16, 2023 Loading…
1
Downgrade duplicate variant error to a warning and skip duplicates.
#71 by susannasiebert was merged Oct 16, 2023 Loading…
1
Output warning when VCF is annotated with the PICK flag but not transcript was PICK'ed
#70 by susannasiebert was merged Oct 16, 2023 Loading…
1
Handle case in the ref-transcript-mismatch-reporter where there is no protein position annotation
#69 by susannasiebert was merged Oct 16, 2023 Loading…
1
1
Prevent ZeroDivisionError errors in log output
#68 by susannasiebert was merged Oct 16, 2023 Loading…
1
1
Update vcf-expression-annotator documentation to clarify custom id-column parameter
#67 by susannasiebert was merged Oct 16, 2023 Loading…
1
3
Update the expression annotator to use the gene (ID) column in Kallisto files
#66 by susannasiebert was merged Oct 16, 2023 Loading…
1
1
Update tests to run in newer Python versions
#64 by susannasiebert was merged Oct 12, 2023 Loading…
fixing typo
#54 by chrisamiller was merged Oct 12, 2023 Loading…
1
Move tests to GitHub actions
#51 by susannasiebert was merged Aug 30, 2021 Loading…
Handle stop_retained_variant, * in wildtype protein sequence, and protein position edge cases
#50 by susannasiebert was merged Aug 30, 2021 Loading…
1
Fix warning message for the VCF expression annotator when running in gene mode
#45 by susannasiebert was merged Apr 26, 2021 Loading…
1
New tool ref-transcript-mismatch-reporter
#44 by susannasiebert was merged Apr 26, 2021 Loading…
1
Add support for adding genotype to an existing single-sample VCF
#41 by susannasiebert was merged Jul 27, 2020 Loading…
1
1
Fix bug with vcf-genotype-annotator that would fail when trying to add a dummy sample to VCFs with existing samples
#40 by susannasiebert was merged Jul 27, 2020 Loading…
1
3
New tool to add new samples with genotype fields to a VCF
#33 by susannasiebert was merged Oct 23, 2019 Loading…
@susannasiebert
Allow --ignore-transcript-version argument to also work on gene identifiers
#29 by susannasiebert was merged Oct 23, 2019 Loading…
1
3
join multiple transcripts with a comma
#26 by apaul7 was merged Apr 24, 2019 Loading…
1
1
clarify input format
#24 by chrisamiller was merged Apr 5, 2019 Loading…
10
Skip complex indels since they are not supported by bam-readcount
#22 by susannasiebert was merged Mar 6, 2019 Loading…
3
Add new tool transform-split-values
#21 by susannasiebert was merged Oct 23, 2019 Loading…
1
9
Port add_annotations_to_table_helper.py script to standalone tool vep-annotation-reporter
#18 by susannasiebert was merged Jan 16, 2019 Loading…
6
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