Hi everyone, I have gotten many responses from the site even though I never asked a question, this is my first query. I am working with ensemble vep to annotate and filter a vcf file. With this script I can annotate and filter the variants:
vep --species homo_sapiens --assembly GRCh37 --offline --xref_refseq --failed 1 --check_existing --no_escape --filter_common --dir $ HOME / .vep --fasta $ HOME / .vep / homo_sapiens / 102_GRCh37 / Homo_sapiens .GRCh37.dna.toplevel.fa.gz --vcf --input_file AML1.vcf -o AML1_vep.vcf
With this script, around 40 variants with population frequencies greater than 1% are eliminated, however there are 7 variants with frequencies greater than 1% that are not removed. I can see that these variants have no data in the AF column which is where the filter acted (filter_common). I tried with --filter "AFR_AF <0.01 or not AFR_AF" and removing --filter_common but got the same result; I got the same variants as with filter_common. Could someone tell me what I'm doing wrong? Thank you very much!