TRTools

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statSTR handling of chrY

1

I get the following error when running statSTR on a VCF with chrY loci genotyped by ExpansionHunter: `File "/root/micromamba/lib/python3.10/site-packages/trtools/utils/utils.py", line 312, in GetHardyWeinbergBinomialTest if gt[1] not in allele_freqs.keys(): IndexError: tuple...

hopedisastro

Converting Beagle imputed VCF for TRTools

5

Hi First of all, thanks for developing TRTools! I have a question regarding imputed STR input files. I have a Beagle (v5.4) imputed VCF file that looks like below: >##fileformat=VCFv4.2...

maegsul

Merge STR: More than one value found for END

1

Im trying to merge around 3 files of GangSTR output into one mergefile. while doing it, Im facing an issue of > More than one value found for END it...

bharathramh

mergeSTR can't merge haploid data from HipSTR output

2

Hi, Recently I have been processing some haploid vcf files from HipSTR output and I find I can't merge haploid data through mergeSTR, and the errors are as follows: TypeError:...

Lidweixiang

```text dumpSTR --vcf output/gangstr/SC074198_chrX.vcf --out output/dumpstr_call/SC074201_chrX --gangstr-min-call-DP 20 --gangstr-max-call-DP 1000 --gangstr-filter-spanbound-only --gangstr-filter-badCI Traceback (most recent call last): File "/data/zhuw10/conda_envs/snakemake/bin/dumpSTR", line 10, in sys.exit(run()) File "/data/zhuw10/conda_envs/snakemake/lib/python3.10/site-packages/trtools/dumpSTR/dumpSTR.py", line 1272, in run retcode...

weizhu365

Hi, Are there default orders of operations in dumpSTR, especially the order between call-level filter and locus-level filter? For example, my command is like: dumpSTR --vcftype gangstr --gangstr-filter-spanbound-only --gangstr-filter-badCI --gangstr-max-call-DP...

bioinfoYY

Logistic regression in AssociaTR

5

Hello! Is there a plan for binary outcome/logistic regression support for AssociaTR? Thanks

asuresh2

DumpSTR: Without --drop-filter, the output shows HET=-1 locus

1

Paddy1401

:robot: I have created a release *beep* *boop* --- ## [6.1.0](https://github.com/gymrek-lab/TRTools/compare/v6.0.2...v6.1.0) (2024-08-29) ### Features * adding the annotaTR tool ([#226](https://github.com/gymrek-lab/TRTools/issues/226)) ([59dd532](https://github.com/gymrek-lab/TRTools/commit/59dd5323b6d58b38abe36836fbfe13f789ff4048)) * support for Apple M1 silicon ([#227](https://github.com/gymrek-lab/TRTools/issues/227)) ([dfec9c2](https://github.com/gymrek-lab/TRTools/commit/dfec9c229955f2862fb796d3d3360d1044f9cdc8)) ###...

github-actions[bot]

This PR introduces multiple options to annotaTR that help with debugging issues that arose when processing large files. 1. Added option `--region` to enable running annotaTR on a specified genomic...

gymreklab