TRTools

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feat: Add longtr support

1

This PR adds explicit support for LongTR VCF files, meaning most commands will now accept `--vcftype longtr`. Because [LongTR](https://github.com/gymrek-lab/longtr) is an extension of HipSTR for long reads, the format is...

gymreklab

Explain how to use GitHub codespaces in our README. A config for our codespace was added in #199, but it wasn't properly documented. This PR also clarifies the purpose of...

aryarm

This PR added an only_passing option to statSTR. Enables the tool to filters out the VCF records with non-passing FILTER column Resolves #162 ## Checklist * [x] I've checked to...

Buuxx

fix: beagle AP field

5

This PR ensures that mergeSTR will output format fields from hipstr-beagle. Specifically, it adds support for the AP1, AP2, and DS fields. Note that only hipstr input is supported for...

nicholema

I used this command `qcSTR --vcf JPZ0127.vcf.gz --out JPZ --quality per-locus --vcftype eh` and get this result > Requested a quality plot, but the input vcf doesn't have quality scores....

jawad9-11

MergeSTR creating multiple duplicate entries in the output

2

I tried to merge two VCF files generated using GangSTR and there are many more entries than the original bed file and found that there are duplicate entries This is...

Dhaksnamoorthy

Add formal support for python 3.13 in our CI

aryarm

:robot: I have created a release *beep* *boop* --- ## [6.2.0](https://github.com/gymrek-lab/TRTools/compare/v6.1.0...v6.2.0) (2025-02-20) ### Features * add `--only-passing` option to statSTR ([#229](https://github.com/gymrek-lab/TRTools/issues/229)) ([51c0481](https://github.com/gymrek-lab/TRTools/commit/51c048191684342737edcc08e58f9d29806d563f)) ### Documentation * add note about bcftools version...

github-actions[bot]

Hi, I was playing around with TRTools to run a GWAS. AnnotaTR is working very nicely together with plink to run a GWAS. I was wondering if it would be...

raphaelbetschart

docs: Add TR GWAS tutorial

4

This PR introduces a new vignette showing how to run a TR GWAS, including TR imputation, computing dosages, and running GWAS with plink2. Not all of these steps use TRTools...

gymreklab