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Command line:
$smoove call --outdir $smooveout --name ${tumor}_${normal} --fasta $ref -p 1 --genotype $tdata/$tumor.MarkDuplicates.bam $ndata/$normal.MarkDuplicates.bam
error:
[smoove] 2020/07/16…
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I can't set in advance, in a workflow, a parameter that is a value filtered from a data table.
It works on tool panel, I can select a species, then the second list holds only databases of this sp…
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Release testing 23.0
Tutorial: https://training.galaxyproject.org/training-material/topics/galaxy-interface/tutorials/collections/tutorial.html
* Mapping reads
- usegalaxy.org's version has 1…
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The current merge module doesn't include SNP rsids during annotation. Since HRC imputed data only includes chromosome and position, this info would be helpful.
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Probably related to #101.
By reading the documentation of SnpEff & SnpSift:
https://pcingola.github.io/SnpEff/examples/
By the way, **I strongly recommend writing such a tutorial before any new…
ysard updated
2 years ago
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Hi there,
Thank you for your program! I've succesfully compiled the code and tested it on the provided examples . However, when testing it on independent data (using hg19.fa and a VCFv4.1 output fr…
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Take as input an unannotated VCF file, and output a VCF file with annotations.
@vlaufer, @erinkwagner, @HuaLing1, if you have time, please comment on which information that @cjav can expect in your o…
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Hello,
I am aware that this question has been asked before, but still I (and others, when looking around in recent posts on Biostars and Seqanswers) have trouble with properly filtering somatic var…
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## WGS (Whole Genome Sequencing)
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I updated the admin stats queries to get the user and usage stats for all time and last 5 years to the date 2024-08-31. Xref: https://github.com/usegalaxy-eu/issues/issues/598
This will provide con…