Gymrek Lab

Problem with read IDs repeated in the same BAM file

6

We get the following error if there is more than one read pair in a given region with the same read ID: ```"ERROR: Failed to extract passes filters tag from...

The option `--gangstr-require-support` went away in conversion to cyvcf2. But is used by at least one of our workflows. It would be nice to bring this back.

Currently, statSTR outputs stats for every locus. It would be convenient to be able to only output stats for loci where FILTER is passing.

I got this error when running on a BAM file with only chr22 extracted but without setting the insert size mean/sdev on the GangSTR command line

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...

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...

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...