Cyriac Kandoth
Cyriac Kandoth
Solid work here. Having VCF output puts this well ahead of other FACETS wrappers I've seen. `cnv_facets` currently uses FACETS `v0.5.14`. Do you have plans to update this? [Here is...
From @knightjimr: "Getting 'uninitialized value' errors for attached VCF file with a variant that triggers the error (on version 1.6.14). This variant has multiple alt alleles, which may be the...
ExAC allele counts and frequencies are already in the VEP cache. But we use the `ExAC_nonTCGA` VCF instead, minus a few known somatic variants related to hematopoietic clonal expansion. Figure...
VCF specs define the breakend format as follows: ``` REF ALT Meaning s t[p[ piece extending to the right of p is joined after t s t]p] reverse comp piece...
The older VEP v86 and v88 seem to work fine with vcf2maf v1.6.15 and generate a proper MAF for the SVs. But VEP v92 with vcf2maf 1.6.16 produces an empty...
Need to support `AF` and/or `DP4` in the genotype columns of [lofreq.vcf](https://github.com/mskcc/vcf2maf/files/2446842/first100lines.vcf.txt) Currently supported genotype FORMATs are: https://github.com/mskcc/vcf2maf/blob/master/vcf2maf.pl#L956-L1031
It's not listed at https://useast.ensembl.org/info/genome/variation/predicted_data.html#consequences but it still shows up in the results of a large project. vcf2maf assigns it the lowest priority by default.
The [current gist](https://gist.github.com/ckandoth/f265ea7c59a880e28b1e533a6e935697) to download the ExAC VCF and whitelist known somatic events, will also inadvertently whitelist indels that overlap these known somatic events. Fixing this will take some work....
This bug has always existed. It happens because `maf2maf` uses `maf2vcf` to create a deduplicated multi-sample VCF for VEP, and `FILTER` tags are necessarily merged across samples. The solution might...
Pulled `mask.bed` files from Illumina's [Alt-Masked-v2 references](https://support.illumina.com/sequencing/sequencing_software/dragen-bio-it-platform/product_files.html) and renamed them to match file names of v1 BED files in dragmap repo.