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Hi, I have an issue with the table splitting in coding and non-coding variants.
Within my dataset there are (germline) variants annotated in their consequence with "frameshift_variation" or even "cod…
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M2 is not picking up on a strand biased variant which is a hom-alt in a bacterial sample.
![Screen Shot 2019-10-11 at 2 30 12 PM](https://user-images.githubusercontent.com/11790802/66675616-a9eed68…
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I get this output in my vcf file
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SAMPLE
Ad-ED119.9_ECJ9+CMV-JnJ-StabWuS-SV40-dsRNA 18587 Sniffles2.INS.3S0 N …
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This ticket aims to get a better handle on how oncogenicity and pathogenicity are related, and the constraints we should model around them with respect to variant origin, the disease object, and the s…
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Hello, I was doing germline analysis following the user guide using cnvkit 0.9.9. However, I have some questions about outputting cnr.
I use the code `cnvkit.py batch B1_bqsr.bam --segment-method hmm…
wqrao updated
2 years ago
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@LeeTL1220 has already made substantial progress on this front, but I think we can improve ground truth sets and expand the number and type of evaluation metrics calculated. To start, this will inclu…
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Hello,
I am trying to incorporate the ensemble approach in my bcbio analysis and getting errors at the bcbio.variation command for validation of calls. Here are some details,
Run log -
/gpfs/ngs/on…
ssaif updated
10 years ago
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Ideally, all warnings or errors should be available from the UI, so that the utility can be run on an unattended server and accessed over the web. However some are not. As an example, I inadvertently …
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Hi,
First of all, we want to thank you for this wonderful application. It has streamlined our variant annotation workflow tremendously.
We submitted the HG19 chr16-11349332-CC-TT variant to Ope…
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I recently read your master piece in JCO. I am interested in your process running SGZ, for detecting potential somatic mutation from germline ones.
In your paper, I saw `Because SGZ does not ship …