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### Submitter Name
Grace Pendlebury
### Submitter Affiliation
Shariant / Australian Genomics
### Submitter Github Handle
_No response_
### Additional Submitter Details
Shariant is…
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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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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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Initial notes on proposed scope and definition of these VA type, based on requirements and considerations documented [here](https://docs.google.com/document/d/1J4AqGDEqyK8KAzfiowgHYKJNvzHuwHSHgkN9dleL…
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### Need
As a geneticist I want to see true variants and not false positive calls. Currently we have databases for annotating variants that are commonly observed as somatic in highly filtered T+N cas…
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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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## Bug Report
### Affected tool(s) or class(es): Mutect2
### Affected version(s)
gatk 4.2.5
### Description
Like most use cases, I acquired a high-confidence, "consensus" VCF from a large …
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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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### Need
As a clinician I want to be able to detect all true somatic variants, but currently in WGS-tumor-only cases we are filtering out all somatic variants with a VAF of 1 with a bcftools filter…
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We initially defined the variantOriginQualifier as refining the statement/annotated knowledge to indicate that it hold for variants of a particular genetic origin (e.g. germline vs. somatic).
It h…