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Hi
I used the following script to convert the GVF file to a VCF file.
https://github.com/hxin/DisEnt/blob/master/disnet/common/lib/ensembl-api/ensembl-variation/scripts/misc/gvf2vcf.pl
My goal…
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Hello:
I am using this library to read a VCF file that has been filtered (GATK Mutect2 + FilterMutectCalls) such as:
> #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT LH0…
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Hello,
I have run CPSR on some germline samples, and am looking at the biomarker section now. I see that class 4 and 5 variants overlapping the CIViC markers are considered, however, the biomarker…
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Hi guys,
I get regular requests from collaborators to look if we have seen germline variants in a specific gene within our AFHCS or GA cohorts. I've created a 'Gene Search' analysis to have a quick…
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Thanks a lot for this great tool. I have some puzzles wanting for help
1 Can it be used for somatic
2 can it call EGFR or other genes complex variants
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Hello,
I would like create a dataset for benchmark somatic variant caller with your software. Thanks for this clear documentation and your well-designed tool ! I just don't fully understand the gen…
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### Submitter Name
Kyle Moad/Rachel Karchin
### Submitter Affiliation
Johns Hopkins
### Submitter Github Handle
kmoad/RachelKarchin
### Additional Submitter Details
We are the PI and an enginee…
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Hi,
We want to use CNVkit for CNV calling on somatic data. What kind of VCF file should we use for best results? Should it contain germline or somatic variants or both? Is there any specific caller…
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Currenty, the user can only classify a variant according to the ACMG guidelines. However, for somatic variants it would be good to also have support for the [ClinGen-CGC-VICC Guidelines](https://pubme…
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Hi everyone,
Can I use this workflow for tumor only variant calling to detect both Somatic and Germline variants? Or should I first run my data with Mutect in tumor only mode and then use varlocira…