TRTools
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gymreklab
Toolkit for genome-wide analysis of tandem repeats
Hi, Thanks for developing this useful tool. I have two questions about understanding the output of qcSTR. 1. In the doc of qcSTR (https://trtools.readthedocs.io/en/latest/source/qcSTR.html):  > Can be used to...
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.
Not sure how to fix the problem, but I performed several different parameter settings, including all the default settings for dumpSTR on the the *.vcf input ( dumpSTR --vcf input.vcf...
Hi Melissa, First off, thanks for the useful toolkit. I'm working with some big datasets and the vectorized pdfs that are created with compareSTR and qcSTR are sometimes too big...
right now, mergeSTR splits the file list by itself. however, argparse can take a list of items (including what is expanded out from a glob, like `*.vcf.gz` in the following...
Currently, statSTR outputs stats for every locus. It would be convenient to be able to only output stats for loci where FILTER is passing.
Hi, I'm trying to compare STR calls from GangSTR and ExpansionHunter using compareSTR. compareSTR was able to run and provide output files but I received the warning below. Why does...
Hello, I encountered the following error when running DumpSTR on a vcf produced by GangSTR that had only chrX calls for 3 samples. Two of the samples are female and...
Pls advise: Is the below an ERROR in my input file, or please advise how I might resolve this ERROR, or further check this ERROR...THANKS! COMMAND LINE: statSTR --vcf adVNTR_MergedFILE...
Which tools can handle haploid data? (GangSTR is one) Are any of these tools not human specific and can handle ploidy >2? For those cases we should add test cases...
