Question : Annotating dbNSFP using snpSIFT , problem with index

Question

[jan]

Hi,

I'm trying to annotate vcf files for dbNSFP using snpSIFT.

I have downloaded the database and index file from the snpSift manual page.

I'm getting error when I run the program

java -jar ~/snpEff_latest_core/snpEff/SnpSift.jar dbnsfp -v -db ~/snpEff_latest_core/snpEff/0B7Ms5xMSFMYlSTY5dDJjcHVRZ3M.gz comb.vcf > out.vcf
00:00:00.000 SnpSift version 4.1k (build 2015-09-07), by Pablo Cingolani
00:00:00.006 Command: 'DBNSFP'
00:00:00.007 Reading configuration file 'snpEff.config'
00:00:01.120 done
00:00:01.121 Annotating
     Input file    : 'comb.vcf'
     Database file : '/home/jannahS/snpEff_latest_core/snpEff/0B7Ms5xMSFMYlSTY5dDJjcHVRZ3M.gz'
Fatal error: Tabix index not found for database '/home/jannahS/snpEff_latest_core/snpEff/0B7Ms5xMSFMYlSTY5dDJjcHVRZ3M.gz'.
      SnpSift dbNSFP only works with tabix indexed databases, please create or download index.

Do I need to do something on the index file that I've downloaded?

Answer 1

[Philipp Bayer]

Does the index file you download end in .gz.tbi?

Most programs expect the index file to be in the same folder and similarly named to the file, so if your database file is (weird name!)

/home/jannahS/snpEff_latest_core/snpEff/0B7Ms5xMSFMYlSTY5dDJjcHVRZ3M.gz

then the tabix index would be

/home/jannahS/snpEff_latest_core/snpEff/0B7Ms5xMSFMYlSTY5dDJjcHVRZ3M.gz.tbi

Maybe you just have to move/rename your downloaded index