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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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`chr3 184714600 Minda_100 N N]chr3:184717314] . PASS SVLEN=2714;SVTYPE=BND;SUPP_VEC=PB_severus_INV4929,ONT_severus_INV5695,ONT_ID_12265_2,PB_ID_53334_2,ILL_95621117:2,ILL_gridss67bb_12113h,ILL_MantaBN…
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Hi,
I have read your paper "Large Drosophila germline piRNA clusters are evolutionarily labile and dispensable for transposon regulation" and am very impressed. I would like to try to see if a simila…
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**Describe the bug**
If there is a heterozygous site in tumor and germline, it should not be called by any somatic caller.
In the case of e.g. 3 reads with sequencing artefacts, VEP will annotate …
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My research is in the direction of a plant and I would like to ask if your model can be migrated to a plant
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Closely related to #201, obviously, but I'm actually more thinking about #317 and efforts to simplify the `Clone` schema. For #201, all `Rearrangement`s/`Cell`s in a `Repertoire` would be nonphysical,…
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Hi,
I have a few questions related to the phasing options.
1. Why is the default SNP panel limited to these variants: "7.4M SNPs with minor allele frequency (MAF) > 0.05:"? If I have tumor data …
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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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Hi Brad,
I am assuming the recall jar uses optimized parameter settings for the variant caller based on bcbio settings. I've been looking at exploring incremental join calling on tumour only samples.…
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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