MTBseq_source
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ngs-fzb
MTBseq is an automated pipeline for mapping, variant calling and detection of resistance mediating and phylogenetic variants from illumina whole genome sequence data of Mycobacterium tuberculosis comp...
Hi. Recently, a new mutation catalogue have been released by WHO: https://github.com/GTB-tbsequencing/mutation-catalogue-2023/tree/main/Final%20Result%20Files I wonder if there is an easy way to renew the MTBseq file https://github.com/ngs-fzb/MTBseq_source/blob/master/var/res/MTB_Resistance_Mediating.txt for to incorporating this...
Hi, Just wondering can draft genomes be used as a reference when running MTBseq ? I am trying to map M. gordonae sequences to the reference genome but there is...
Hi all! I analysed some samples that contain a mutation related with amikacin resitance, checked by other laboratoy techniques, but when I obtain amended results file, this mutation (genomic coordinate...
Hello, thanks for the pipeline I' want to use different reference and needed to convert annotations as suggested in documentation. To get the feel about the annotation format, I've looked...
I'm currently facing an issue with the output files while using MTBseq version 1.0.3 via Docker for analyzing 39 different tuberculosis samples. Here's a breakdown of the steps I've taken:...
Recently I try to install MTBseq and encounter the following issue: Downloading and Extracting Packages: Preparing transaction: done Verifying transaction: - SafetyError: The package for mtbseq located at /home/yang/miniconda3/pkgs/mtbseq-1.1.0-hdfd78af_0 appears...
Hi, this is more a question than an issue. I am just wondering will there be an update of MTBseq anytime soon with the revised WHO mutation catalogue. Cheers, P
Amend
Hi all, the TBAmend step require a lot of time in case of several inputs. I am wondering whether there an option in TBAmend by which adding new samples in...
I was getting this error: ``` ##### ERROR MESSAGE: Invalid command line: Malformed walker argument: Could not find walker with name: RealignerTargetCreator ``` Tracked it down to here: https://gatkforums.broadinstitute.org/gatk/discussion/10464/invalid-command-line-malformed-walker-argument it...
**Issue:** Working with GATK 3.8 is a hassle. It requires download the jar and registering it separately due to licensing issues. This limits the ease of installation and distribution of...
