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Dear all,
In order to compare with `GATK`, I also called the variants using `ANGSD` with following command which can report the homozygous for alternative alleles. But I found the `ANGSD` have exc…
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I'm using HaplotypeCaller (`gatk-package-4.beta.5`) to analyse the control medulloblastoma sample from the ICGC benchmark https://www.nature.com/articles/ncomms10001. Reads are aligned to `GRCh37` (fr…
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as identified in https://github.com/edamontology/edamontology/issues/292#issuecomment-314162572
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We have a sort in the INDEL realigner that takes most of the realignment time. We do this so that we can get the full alignment position of all reads that cover a target, but this is actually an unnec…
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Upon trying to redeploy bespin-web, the server process starts but attempts to list jobs result in a 500 error due to a failed migration
```
ProgrammingError: column data_job.vm_volume_name does no…
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This is likely intentional but we should still show these parameters in the #docs.
Test command:
```
WMCF9-CB5:hellbender-protected shlee$ ./gatk-launch Mutect2 -I ~/Documents/workshop_materials…
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This derives from a bug report in GATK 3.5 where we found that using -allowNonUniqueKmersInRef rescued real sites. Several other cases have been reported (see original issue linked below). We'd like t…
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Hi
What would be the best way to output active regions from GATK4 HaplotypeCaller?
In GATK 3.x, an option `--activeRegionOut ` could be used to write active regions in a TSV file. However, I am …
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Hi,
I get the following error in the bcbio-nextgen.log:
[2016-11-09T20:36Z] node040: Unexpected error
Traceback (most recent call last):
File "/pico/work/ELIX_prj6/lfarina0/bcbio/data/anac…
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Any plan on this? Thanks