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Ivo suggested that this problem variant, which comes from LOVD but gets spit out by the pipeline, is an artifact of our variant merging process. Let's doublecheck that. Looking at it, it appears to …
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In GitLab by @falquaddoomi on Mar 28, 2019, 07:15
(These notes need to be unpacked into individual sub-issues; I'm putting the full text here to more easily keep track of that.)
changes for SVIP (pr…
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refer to [commit 7d7d291](https://github.com/ding-lab/CharGer/tree/7d7d2911b89261fa5dceea6395a5d188a82757f2)
I remove entire anaconda2 directory
`rm ~/anaconda2`
`mkdir ~/CharGer`
`cd ~/Char…
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vep command:
~/VEP/ensembl-vep/vep --assembly GRCh38 --cache --dir_plugins /home/yubau/.vep/Plugins --everything --fasta /home/yubau/.vep/homo_sapiens/99_GRCh38 --force_overwrite --fork 48 --format v…
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this is because choosen
"unstudied variant…
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these CPT2 variants in case 2007 are both classified with ACMG but only for one of them…
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#### What are the scientific goals of the analysis?
Filter germline variants for deleterious variants within _TP53_, _SUFU_, and _PTCH1_ to enable #247
#### What methods do you plan to use to…
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Hi,
I am running a single tumor only analysis using mutect and vardict. I think this issue is similar to https://github.com/bcbio/bcbio-nextgen/issues/2567 - it appears there is some malformed d…
waemm updated
4 years ago
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Hello,
I tried to use CharGer on a WES vcf file processed with GATK 4.1.1.0 from hg38 bam files and annotate wih VEP 95. VCF contains 547 samples. Looking a the results all variant are classified a…