Missing some predictions based on dbNSFP v4.2a
Hello everybody,
I used dbNSFP v4.2a database for functional prediction and variant annotation. As mentioned in the download site sites.google.com/site/jpopgen/dbNSFP, this version compiles prediction scores from several prediction algorithms (SIFT, SIFT4G, Polyphen2-HDIV, Polyphen2-HVAR. ….), and other information, including allele frequencies observed in the gnomAD data.
After annotation using snpeff & snpsift (please see commands below), I did not get all the information mentioned in dbNSFP v4.2a. For example certain variants are known to be present in gnomaAD but the results obtained do not contain any information about gnomAD.
java -jar snpeff.jar -v hg38 myFile.vcf > myFile.ann.vcf
java -jar SnpSift.jar dbnsfp -v -db path/to//dbNSFP4.2a.txt.gz myFile.ann.vcf > myFile.ann.dbnsfp.vcf
Are there additional steps to annotate the variants with all the scores and data mentioned in dbNSFP v4.2a?
thanks in advance
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