Closed SophiaMurat closed 3 years ago
Hi, I would re-index your CADD file with tabix then check if you can do queries on it from the command line, like:
# index
tabix /data/users/smuratel/cadd/CADD_v1.6_hg38_whole_genome_SNVs.tsv.gz
# query
tabix /data/users/smuratel/cadd/CADD_v1.6_hg38_whole_genome_SNVs.tsv.gz chr2:47783349-47783350
if that is working then vcfanno should work as well. ( you should see, e.g. PHRED=1.23 added to your INFO field)
Thank you for your quick answer! It solved my problem. Everything is now working. Best, Sophia
Hello,
Thank you for this nice tool. I am trying to annotate my vcf with CADD using your tool. When I launch the vcfanno tool, a file is created. In this new vcf file a line was added in the header :
##INFO=<ID=PHRED,Number=1,Type=Float,Description="calculated by mean of overlapping values in column 6 from /data/users/smuratel/cadd/CADD_v1.6_hg38_whole_genome_SNVs.tsv.gz>
But when I look at the info field I do not find the CADD score.Could you tell me if it is normal. If yes, where is the CADD score?
Here are some infos on my setup:
My cadd.conf file:
Here the first lines of the CADD file : CADD_v1.6_hg38_whole_genome_SNVs.tsv.gz
Here one line from my initial vcf file :
chr2 47783349 . G A 1916.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.908;DP=218;ExcessHet=3.0103;FS=1.077;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=9.40;ReadPosRankSum=-0.676;SOR=0.780 GT:AD:DP:GQ:PL 0/1:104,100:204:99:1924,0,2227
Here my command line :
vcfanno -p 2 cadd.conf test.vcf > test.anno.vcf
and here the message from vcf anno :
Thank you in advance for your answer.
Best regards,
Sophia