few variants annotated with dbSNFP3.5a
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22 months ago
Myosotis1979 ▴ 10

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

vcf variant dbSNP sbNSFP • 376 views
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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.
code_formatting

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.

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Many thanks. I use SnpSift for variant annotation

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