VEP is very slow. Fork doesnt seem to work
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7 weeks ago
nhaus ▴ 30

I am using VEP (v103) to annotate a small vcf file (~1000 variants). Nonetheless, it takes very long (>20 minutes) , which doesnt quite match their description of:

Set up correctly, VEP is capable of processing around 3 million variants in 30 minutes

Furthermore, it seems like the --fork does not really work, because the whole time just one cores is used.

This is the command that i used:

vep  --cache --dir_cache vep-cache --offline --fasta ref-genome.fa --pick --fork 4 --sift b --variant_class -i somatic.filtered.snp.vcf -o snp_vep_out.txt

Id be very thankful if someone could point out what I am doing wrong.

vep annotation • 168 views
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I'm not a VEP user, but if you can't figure it out then you can always use another variant annotator like OpenCRAVAT. My experience is that it should only take several seconds to annotate 1000 variants (docs here: https://open-cravat.readthedocs.io/en/latest/ ).

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Also, as it looks like you are trying to annotate somatic mutations (likely in cancer), OpenCRAVAT has more options for predicting oncogenic mutations in cancer beyond sift. Most recent benchmarks suggests there are many other better methods for cancer (https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-01954-z ).

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7 weeks ago

I assume you've already seen this documentation page based on the quote at the top. The 3M in 30 min is really the absolute fastest under ideal conditions, which means no additional flags (--pick and --sift in your command will make it slower).

Please check that your input file is sorted and that you've tabix-indexed your cache.

With regard to forking, the VEP automatically reads 5000 variants to memory in each fork, so there will be no forking if you have <5000 variants. You can change this with --buffer_size but I doubt this would increase speed much.

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