Cyriac Kandoth

Thanks for reporting this. It looks like a VEP runtime error. It was either not installed fully or had an un-handled exception. Let me know if you are still having...

Hi @ISmolicz. The `--max-subpop-af` option cannot be deactivated, but it is trivial to remove the `common_variant` tag in a downstream step. It is also trivial to filter based on specific...

maftools is a great choice for filtering. Stick with that. 1. Good point - VEP only caches the gnomAD exome allele frequencies, not the gnomAD genomes, probably because it was...

Thanks. I agree - vcf2vcf's genotyping feature should be sped up with a BED file. I use a similar strategy to speed up `samtools faidx` to [pull flanking bps](https://github.com/mskcc/vcf2maf/blob/v1.6.16/vcf2maf.pl#L361-L376). But...

To fix this, the hotspots events need to be in VCF format, but the downside is that we miss novel ALT alleles at known hotspot loci. Tough tradeoff.

All the hotspots and allele changes observed in a MAF-like format here - https://github.com/mskcc/ngs-filters/blob/master/data/hotspot-list-union-v1-v2.txt

Your goal is confusing. What is the input format you have? And what is the output format you want?

ok thanks. In a standard VCF, the read counts and REF/ALT allele counts are usually in columns named after sample IDs. If you specify the correct sample IDs using arguments...

Thanks @rhshah. @inodb can you review your python notebook and help figure this out? The issue might be in biomart. WT1 has a uniprot entry here - http://www.uniprot.org/uniprot/P19544

WT1 is now included in `isoform_overrides_uniprot`. @inodb do you still need `isoform_overrides_uniprot_from_biomart_91` to live separately, or can I remove it? Not all those isoforms may be available for GRCh37 users.