<div dir="ltr">Hello,<div><br></div><div>As you've seen, this data can be somewhat confusing.</div><div><br></div><div>The GMAF field always reports the minor allele frequency, whereas the other frequency fields report the frequencies of the ALT (or ALTs if there is more than one).</div><div><br></div><div>Ideally the VEP would report the frequency of the ALT allele that you input in your VCF, but this raises further problems if the ALT allele you report does not match either the REF or ALT alleles from the 1000 Genomes VCF. It is something we are hoping to improve in a future VEP release.</div><div><br></div><div>For your second question, it looks like frequencies have been mistakenly assigned to the two reported co-located variants (<span style="font-size:12.8000001907349px">rs3902057 and </span><span style="font-size:12.8000001907349px">RISN_CRB1:c.1410A>G), so the frequencies appear twice. We'll look into a fix for this.</span></div><div><span style="font-size:12.8000001907349px"><br></span></div><div><span style="font-size:12.8000001907349px">Regards</span></div><div><span style="font-size:12.8000001907349px"><br></span></div><div><span style="font-size:12.8000001907349px">Will McLaren</span></div><div><span style="font-size:12.8000001907349px">Ensembl Variation</span></div></div><div class="gmail_extra"><br><div class="gmail_quote">On 29 May 2015 at 14:29, Svein Tore Koksrud Seljebotn <span dir="ltr"><<a href="mailto:s.t.seljebotn@medisin.uio.no" target="_blank">s.t.seljebotn@medisin.uio.no</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi,<br>
<br>
I am trying to figure out some of the output I get from VEP (version 79) when annotating vcf files. See end of email for input and command. Please note, I am new to this field, so I might misunderstand a few concepts...<br>
<br>
For the variant (1 197390368 rs3902057 A G) I get the following output:<br>
<br>
CSQ=G|upstream_gene_variant|MODIFIER|CRB1|ENSG00000134376|Transcript|ENST00000480086|processed_transcript||||||||||rs3902057&RISN_CRB1:c.1410A>G|1|1573|1|HGNC|2343||||||||A:0.0803|G:0.7065&G:0.7065|G:0.9813&G:0.9813||G:1&G:1|G:0.999&G:0.999|G:1&G:1|G:0.7696&G:0.7696|G:0.9986&G:0.9986|||19339744|||| {rest of transcripts omitted...}<br>
<br>
- This might be a silly question, but why is GMAF given for REF, while the subpopulations are given for ALT? In my case I'm interested in the frequency for the ALT, not the REF. I assume it's giving the minor allele frequency always? But why is there a difference in the allele given for GMAF vs e.g. AFR_MAF?<br>
<br>
Looking at a later transcript for same variant, I see the following:<br>
<br>
G|synonymous_variant|LOW|CRB1|23418|Transcript|NM_001193640.1|protein_coding|4/10||NM_001193640.1:c.1074A>G|NM_001193640.1:c.1074A>G(p.=)|1283|1074|358|L|ctA/ctG|rs3902057&RISN_CRB1:c.1410A>G|1||1|||||NP_001180569.1|rseq_mrna_nonmatch&rseq_cds_mismatch&rseq_ens_match_cds||||A:0.0803|G:0.7065&G:0.7065|G:0.9813&G:0.9813||G:1&G:1|G:0.999&G:0.999|G:1&G:1|G:0.7696&G:0.7696|G:0.9986&G:0.9986|||19339744||||,G|5_prime_UTR_variant|MODIFIER|CRB1|ENSG00000134376|Transcript|ENST00000367397|protein_coding|2/6||ENST00000367397.1:c.-448A>G||411|||||rs3902057&RISN_CRB1:c.1410A>G|1||1|HGNC|2343|||ENSP00000356367|||||A:0.0803|G:0.7065&G:0.7065|G:0.9813&G:0.9813||G:1&G:1|G:0.999&G:0.999|G:1&G:1|G:0.7696&G:0.7696|G:0.9986&G:0.9986|||19339744||||<br>
<br>
- Why is the frequency for the subpopulation alleles repeated twice with same value? Why not always give the frequency for all alleles?<br>
<br>
<br>
Best regards,<br>
Svein Tore Koksrud Seljebotn<br>
<br>
<br>
<br>
<br>
**** Example VCF: *****<br>
<br>
##fileformat=VCFv4.1<br>
##INFO=<ID=class,Number=.,Type=String,Description="class"><br>
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"><br>
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT H02<br>
1 197390368 rs3902057 A G 7128.77 . AC=2;AF=1.00;AN=2;DB;DP=193;Dels=0.00;FS=0.000;HaplotypeScore=4.6974;MLEAC=2;MLEAF=1.00;MQ=70.00;MQ0=0;QD=29.21 GT:AD:DP:GQ:PL 1/1:0,192:193:99:7157,518,0<br>
<br>
***** Command: *****<br>
vep --cache --dir_cache=/work/VEP/cache/ --fasta=/work/human_g1k_v37_decoy.fasta --offline --sift=b --polyphen=b --ccds --hgvs --numbers --domains --regulatory --canonical --protein --biotype --gmaf --maf_1kg --maf_esp --pubmed --allow_non_variant --fork=4 --vcf --allele_number --no_escape --failed=1 --no_stats --merged --symbol -i testfile.vcf -o testfile.annotated.vcf<br>
<br>
<br>
_______________________________________________<br>
Dev mailing list <a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a><br>
Posting guidelines and subscribe/unsubscribe info: <a href="http://lists.ensembl.org/mailman/listinfo/dev" target="_blank">http://lists.ensembl.org/mailman/listinfo/dev</a><br>
Ensembl Blog: <a href="http://www.ensembl.info/" target="_blank">http://www.ensembl.info/</a><br>
</blockquote></div><br></div>