TBProfiler
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jodyphelan
Profiling tool for Mycobacterium tuberculosis to detect ressistance and strain type from WGS data
Hello, I came across an error with the Pathogen Profiler [combine_vcf_variants.py](https://github.com/jodyphelan/pathogen-profiler/blob/master/scripts/combine_vcf_variants.py) script that seems to occur in approximately half of my samples with TBProfiler v6.2.0. The same samples previously ran...
# tb-profiler error report * OS: linux * Program version: 4.4.2 * Database version: c2fb9a2 * Program call: ``` {'read1': '/etc/ace-data/home/sbabirye/data/fastq_Seq/ERR038736_LIB1_R1.fastq.gz', 'read2': '/etc/ace-data/home/sbabirye/data/fastq_Seq/ERR038736_LIB2_R2.fastq.gz', 'bam': None, 'fasta': None, 'vcf': None, 'platform':...
Hello, Tb-profiler version v6.2.0 is not reporting "missing positions report" data in the .txt output (default settings). The data is generated in the .json file but in the .txt is...
Hello, I have a MTB strain with a large deletion in pncA gene, that should leed to LoF. In a previous version of tb-profiler this deletion reported resistance to Pyrazinamide...
Hello, Tb-profiler v6.2.0 calls a variant in fbiC at 100% frequency, with associated resistance to Delamanid and Pretonamid, that only exists in 2 or 3 reads. 1305494 Rv1173 fbiC frameshift_variant&stop_lost&splice_region_variant...
b-profiler collate [04:57:16] INFO Using ref file: /home/p0129674/anaconda3/envs/my_pro/share/tbprofiler//tbdb.fasta db.py:594 INFO Using gff file: /home/p0129674/anaconda3/envs/my_pro/share/tbprofiler//tbdb.gff db.py:594 INFO Using bed file: /home/p0129674/anaconda3/envs/my_pro/share/tbprofiler//tbdb.bed db.py:594 INFO Using version file: /home/p0129674/anaconda3/envs/my_pro/share/tbprofiler//tbdb.version.json db.py:594 INFO Using json_db...
I am trying to run a TBProfiler 4.2.0 analysis on our Linux HPC cluster using trimmed, aligned, and deduplicated bam files as input (-a option). All of my runs have...
Hello, when I use the 4.3.0 version of tb-profiler to run the ERR2184272 sample, The command is as follows: `tb-profiler profile -1 ERR2184272_1.fastq.gz -2 ERR2184272_2.fastq.gz -t 2 -p ERR2184272 --csv`...
On v6.2.0, I run: `tb-profiler update_tbdb --match_ref myref.fna` I get: ``` ValueError: Command Failed: /bin/bash -c set -o pipefail; tb-profiler create_db --prefix tbdb --csv mutations.csv --watchlist watchlist.csv --rules rules.txt --match_ref...
Hello! It seems that some mutations in the tbdb.barcode.bed file are not based on H37Rv's coordinates. Could you clarify which ones have a different reference coordinates? Thank you
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Profiling tool for Mycobacterium tuberculosis to detect ressistance and strain type from WGS data