Variant Effect Predictor warnings Chromosome 'p' not found in cache

Question

[bruce.moran]

Hi,

I am trying to run VEP, have installed it using the perl INSTALLER.pl which completed fine, using v79, for humans on build GRCh37. I have VCFs called with GATK. The error is for each line:

WARNING: Chromosome 'P' not found in cache on line 'L'

where 'P' is all chromosomes, 'L' all lines of VCF.

So I imagined the error was that Ensembl fasta was chromosomes named 'P', versus my own 'chrP', so I changed my VCF, still get error. Changed fasta, VEP creates a new index and still get warnings. So I thought I would ask. What format does VEP want? Google reveals nothing on this error. Sample of my VCF below:

chrY    28600094        .       A       G       52.77   .       AC=1;AF=0.500;AN=2;BaseQRankSum=-7.360e-01;ClippingRankSum=-7.360e-01;DP=3;FS=0.000;GQ_MEAN=36.00;MLEAC=1;MLEAF=0.500;MQ=51.09;MQ0=0;MQRankSum=-7.360e-01;NCC=0;QD=17.59;ReadPosRankSum=0.736;SOR=0.223     GT:AD:DP:GQ:PGT:PID:PL      0/1:1,2:3:36:0|1:28600094_A_G:81,0,36

Thanks for help in advance=)

[bruce.moran]

Hi Will,

files were there originally as you show, I did a clean reinstall and it is working now. Thanks for your help.

Answer 1

[EnsemblWill]

Probably there was an issue setting up the cache; if it reports they are all missing, then chances are the files genuinely aren't there.

If you used INSTALL.pl and the default parameters, you should see a bunch of files in each chromosome directory, e.g.

ls $HOME/.vep/homo_sapiens/79_GRCh37/Y/ | head
10000001-11000000.gz
10000001-11000000_reg.gz
10000001-11000000_var.gz
1000001-2000000.gz
1000001-2000000_reg.gz
1000001-2000000_var.gz
1-1000000.gz
1-1000000_reg.gz
1-1000000_var.gz
11000001-12000000.gz

Check that you have enough disk space where you are putting the cache files, then try running the installer again to get the cache.

Finally, VEP doesn't care whether the VCF has "chrY" or "Y", it changes this internally for you. However, the names in the FASTA file must be consistent with the cache file, so please try and use the cache and FASTA provided by Ensembl where possible.

[jimhavrilla]

Thank you Will, I had the same error, and restoring the cache (which was flawed somehow) definitely fixed it.