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Need a class that represents disease mutations (genetic variants, mendelian disease mutations, complex disease variants, cancer autosomal and somatic variants) that are mapped to `Position` and `Resid…
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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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Hello,
When I run strelka2 somatic variants calling with "--reportEVSFeatures", I got variants vcfs containing values of "TumorSampleAltAlleleFraction". Those values are very close to "Somatic all…
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**Describe the bug**
An analysis on UMI cancer paired data with the option below, all somatic variants present LBQ filter at least. It's odd because on an the same analysis but with default filtering…
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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…
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After doing somatic variant calling, the AD shows that the alternate allele is supported by three to five reads out of typically about eighty reads for almost all of the variants and the patient has a…
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For normal-tumor sample pair, when I run with somatic mode, I got a somatic variant in which normal variant allele frequency was 0.0526.
1 241680511 . T TA . PA…
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Hi!
I have WES with ~30x coverage, matched normal-tumor samples and I am interested in somatic mutations. Unfortunately, it is not clear for me, what kind of vcf file should I use as an input for snp…
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We are following the example here and noticed the following overlap with the example data between somatic SNV calls made from scRNAseq with v1.0 and v1.6.
![image](https://github.com/KChen-lab/Mono…
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`chr10 67470511 Minda_11 N N]chr10:68211499] . PASS SVLEN=740988;SVTYPE=BND;SUPP_VEC=ILL_MantaDUP:TANDEM:170154:0:1:0:0:0,ILL_gridss174bf_4460h,PB_severus_BND783_2,ONT_severus_BND834_2,ILL_2795390560:…
jzook updated
1 month ago