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I was looking at the “unknowns” and thought it was odd to see these 'unknown' genes annotated to
“regulation of cell size”
100.00% 48.00 YCR061W, YBR093C, YGR111W
I don't think we should ann…
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This came up in a side discussions [here](https://github.com/airr-community/airr-standards/issues/246#issuecomment-587962477) and [here](https://github.com/airr-community/airr-standards/issues/320#iss…
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This issue arose in the ticket here: https://github.com/ga4gh-gks/variant-annotation-model/issues/22#issuecomment-452561137. In pathogenicity interpretation sources such as ClinVar, it is common for …
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Can an option be added to the main function to consider A1 as the effect allele instead? I have attempted to this manually, but it is inelegant without manipulating scripts contained within the MungeS…
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After marking dupes, the following
biscuit pileup -q 16 -r hg19.fa -i WGBS_$SAMPLE.mkdups.hg19.bam -o WGBS_$SAMPLE.mkdups.hg19.vcf
fails on a number of samples (4/6, not all though). Is there a st…
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Hello,
Is GREEN-VARAN compatible with VCFs annotated by VEP?
Thanks,
Madeline
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Hi,
I'm trying to run McClintock for a large number of isolates. I submitted the first batch of 20 and they all failed with the same error message with malformed bed entries:
```
PROCESSING …
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Hi,
Thanks for the great tool. I got the following variant lines. I wonder how should I handle them since they are germline calls. The input bam consist of only disease causing tandem repeat region…
ghost updated
3 months ago
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Dear developer,
Hello, I encountered some issues while using MixMHC2pred webserver. For the first block, which is used to predict binding specificity, after entering an existing allele in the text …
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Hi!
I'm wondering how to use the new GATK4 copy number segmentation as input to TITAN. I guess it should be possible (see eg. https://software.broadinstitute.org/gatk/documentation/article?id=11088…