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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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`chr18 22492810 Minda_59 N . PASS SVLEN=730112;SVTYPE=DUP;SUPP_VEC=PB_severus_DUP2962,PB_r_191,ONT_severus_DUP3355,ONT_r_113,ILL_MantaDUP:TANDEM:239447:0:1:0:0:0,PB_ID_40649_2,ONT_ID_69814_2,ILL_2890…
jzook updated
1 month ago
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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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e.g. B2M, TAP, &c.
Identifying loss in MHC might require running a custom program which first does genotyping of the germline MHC and then calls somatic variants against those specific alleles.
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`chr1 151220118 Minda_3 N . PASS SVLEN=172;SVTYPE=DEL;SUPP_VEC=PB_ID_3854_2,PB_d_19,ONT_ID_6037_2,ONT_d_11,ILL_MantaDEL:14640:0:1:0:0:0,PB_severus_DEL354,ONT_severus_DEL353,ILL_2186766853:2,ILL_grids…
jzook updated
2 months ago
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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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It has clinical value to note compound variants for cancer as a two-hit model, not only recessive disorders.
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### Description of feature
See https://github.com/broadinstitute/gatk/issues/7606 and #592.
In the GATK4 GetPileupSummaries code, the entire -V option populated by the sarek germline_resource para…
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Hi, I would like to know if lumpy can be also used to call germline and short variants, or its use for such situations is not recommended.
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Funcotator is producing erroneous protein predictions for some variants.
A few include the following from `HG38` using `funcotator_dataSources.v1.6.20190124g.tar.gz`:
```
chr7 48227340 . CTTT…