STRetch
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Oshlack
Method for detecting STR expansions from short-read sequencing data
One or more parallel stages aborted. The following messages were reported: --------------------------------- median_cov_region ( 11_L001 ) ---------------------------------- Command in stage median_cov_region failed with exit status = 2 : set -o...
Hi, I am trying to run the exome pipeline. When I run it for 2 or 3 samples it runs correctly. But, when I run a command for about 20...
Hi, When I run "../tools/bin/bpipe run -p EXOME_TARGET="SCA8_region.bed" ../pipelines/STRetch_exome_pipeline.groovy *.fastq.gz" for testing, it return such errors: File "/opt/STRetch/tools/miniconda/envs/STR/lib/python3.7/site-packages/Bio/Alphabet/__init__.py", line 21, in "Bio.Alphabet has been removed from Biopython. In many cases,...
Hi team, Hope you are all well. Recently we've been trying to install STRetch into HPC system. But it continues to fail. Please see the error message below. ``````````` [dleo2939@login3...
Dear friend: I have successfully installed the software, but when I run the pipeline with the following command line: ------------ pipeline="/work/Software/STRetch-master" bampath="/work//bam" $pipeline/tools/bin/bpipe run $pipeline/pipelines/STRetch_exome_bam_pipeline.groovy $bampath/A.recaled.bam $bampath/B.recaled.bam $bampath/C.recaled.bam $bampath/D.recaled.bam ------------...
Set mosdepth in pipeline_config (via install script) rather than referring to it in pipeline_stages as `$STRETCH/tools/bin/mosdepth`
Have the locus_counts script also report STR_coverage (from the bam index and additional both in pair on decoy calculations) Use counts of read where both in the pair map to...
Hi, I'm eager to try this tool, but I'm a bit unpleasantly surprised by the [installation instructions](https://github.com/Oshlack/STRetch/wiki/Installing-STRetch). I already have anaconda installed - but it seems that it's required to...
https://github.com/brentp/goleft/blob/1137ebe531e67d0d081cdb1900d1ec065501f246/HISTORY.md
