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mskcc / vcf2maf

Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms
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gnomad and esp AF deprecated in VEP v107 #322

Open prmac opened 2 years ago

allaway commented 2 years ago

I experienced this as well for --esp_af. I don't believe --af_gnomad is deprecated but vep 107 failed to recognize the --af_esp flag and threw an error.

I made a small change as a workaround in #328 : https://github.com/mskcc/vcf2maf/pull/328/files

allaway commented 2 years ago

(I now see that someone already filed a PR with the same change in #324).

For the record, this is the error message I see: 

(base) bash-4.2# perl vcf2maf.pl --input-vcf /workdir/vcfs/test.Strelka.filtered.vcf --output-maf /workdir/test.vep.maf --ref-fasta /workdir/fasta/Homo_sapiens_assembly38.fasta --vep-path /root/miniconda3/envs/vcf2maf/bin --vep-data /workdir/vep --ncbi-build GRCh38
STATUS: Running VEP and writing to: /workdir/vcfs/test.Strelka.filtered.vep.vcf
Unknown option: af_esp
ERROR: Failed to parse command-line flags

ERROR: Failed to run the VEP annotator! Command: /root/miniconda3/envs/vcf2maf/bin/perl /root/miniconda3/envs/vcf2maf/bin/vep --species homo_sapiens --assembly GRCh38 --no_progress --no_stats --buffer_size 5000 --sift b --ccds --uniprot --hgvs --symbol --numbers --domains --gene_phenotype --canonical --protein --biotype --uniprot --tsl --variant_class --shift_hgvs 1 --check_existing --total_length --allele_number --no_escape --xref_refseq --failed 1 --vcf --flag_pick_allele --pick_order canonical,tsl,biotype,rank,ccds,length --dir /workdir/vep --fasta /workdir/fasta/Homo_sapiens_assembly38.fasta --format vcf --input_file /workdir/vcfs/test.Strelka.filtered.vcf --output_file /workdir/vcfs/test.Strelka.filtered.vep.vcf --offline --pubmed --fork 4 --polyphen b --af --af_1kg--af_esp --af_gnomad --regulatory
allaway commented 4 months ago

@ckandoth - I believe this issue is resolved with #324, but please correct me if I am wrong!