few variants annotated with dbSNFP3.5a

Question

[Myosotis1979]

Dear all

I'm trying to annotate 400000 variants in a vcf file with dbNSFP3.5a using the hg19 human version. In order to use the hg19/GRCh37, I handled the dbNSFP3.5a.zip with the following commands:

unzip dbNSFPv3.5a.zip
head -n1 dbNSFP3.5a_variant.chr1 > h
cat dbNSFP3.5a_variant.chr* | grep -v ^#chr | awk '$8 != "."' | sort -k8,8 -k9,9n - | cat h - | bgzip -c > dbNSFP_hg19.gz
tabix -s 8 -b 9 -e 9 dbNSFP_hg19.gz

Neverthless, I only got 0.36% annotated with this database (using both dbSNP151 and dbSNP150), which is very lower compared to the annotation with the dbNSFP2.9.txt.gz database (15.96%)(using also both dbSNP151 and dbSNP150).

Can anybody help me to figure out this problem?

Thanks

[Ram]

Please use the formatting bar (especially the code option) to present your post better. You can use backticks for inline code (`text` becomes text), or select a chunk of text and use the highlighted button to format it as a code block. I've done it for you this time.

Also, you have not mentioned the tool you're using to annotate the VCF file. This information is highly relevant to the question at hand.

[Myosotis1979]

Many thanks. I use SnpSift for variant annotation