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Following [my misfortunes with trying to extend the Dcmstack interface](https://github.com/nipy/nipype/issues/1097), I am setting out to wrap a function of my own in place of Dcmstack's `parse_and_sta…
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Hi I am trying to run ABRA on Tumor Normal Pairs, but I am trying to create a custom bed file by running GATK's FindCoveredIntervals tools. The reason to do this is that we want to run ABRA also on o…
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I am trying to run ABRA after using sorting and marking duplicates with PICARD. In the .log file, it seems that ABRA worked well until it needed to call bwa, and I get the following error in the .log…
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Currently, the `transform` command from the CLI only uses the default indel realigner arguments.
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1. réaligner les fréquences
2. sélectionner les participes
gboye updated
9 years ago
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Greetings! I am encountering a java error when running abra. I thought the problem was that my regions are too small (smaller than kmer). I have a de novo genome, and I am interested in coding indels…
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Currently, the indel realigner will throw an error if we don't identify any regions as targets for realignment.
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The indel realigner will attempt to realign areas of the genome which haven't been attached to a target, which can cause errors where we try to reconstruct a reference with an (expected) gap.
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Hello,
I tried to upload a VCF file (3.7 MB) which has caused _Failed: Bad Request (400)_ with the following Dockerfile:
```
FROM bgruening/galaxy-stable:dev
MAINTAINER auto script
ENV GALAXY_CONFIG_…
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Hi Kay! Was looking for a plugin that can generate / update sequences but didn't find anything in the plugin repository. Shifter was the closest to the search, looks pretty awesome and mature, so I th…