search

pcingola / SnpSift

Other
33 stars 20 forks source link

dbNSFPv4.1a database does not index using tabix #54

Closed kgandh2 closed 3 years ago

kgandh2 commented 3 years ago

Hi there - I have downloaded dbNSFPv4.1a from the website and am trying to create a database for snpSift to use. I followed the instructions on this page. https://pcingola.github.io/SnpEff/ss_dbnsfp/

However, tabix is not able to index the file and throws error below [get_intv] the following line cannot be parsed and skipped: Binary file (standard input) matches [ti_index_core] the indexes overlap or are out of bounds

It appears like there are multiple records for one genomic position for different alternate alleles. I have tried to sort the file, check for empty lines and check for complete duplicate lines.

Please help.

Thank you, Kuki

pcingola commented 3 years ago

The file from that page (see "Database" section) is already indexed, the tabix index file should be downloaded alongside the original dbNSFP file (you have to download two files).