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