% vtools show format rsname
Import variants (chr, pos, ref, alt) that are queried from dbSNP database
using provided rsnames
Columns:
None defined, cannot export to this format
variant:
chr Obtain chromosome from dbSNP by rsname
pos Obtain position from dbSNP by rsname
ref Obtain reference allele from dbSNP by rsname
alt Obtain alternative allele from dbSNP by rsname
Format parameters:
sep delimiter used to separate input fields (default: ',')
rsname_col Index for the column with rsname (default: 1)
dbfile Name of an attached dbSNP database or path to the
dbSNP database in sqlite format (default: dbSNP-
hg19_138.DB)
This format retrieves variant information from dbSNP. To use this format, you should first download and decompress the dbSNP database
% vtools init format rsname
% vtools use dbSNP-hg19_138
You can then use the database to import variants from a list of rsnames:
% vtools import variants.txt --format rsname --build hg19
INFO: Importing variants from variants.txt (1/1)
variants.txt: 100% [==================================] 25,462 9.6K/s in 00:00:02
INFO: 25,944 new variants (25,885 SNVs, 50 insertions, 11 deletions) from 25,462 lines are imported.
WARNING: Sample information is not recorded for a file without genotype and sample name.
Importing genotypes: 0 0.0/s in 00:00:00
Copying samples: 0 0.0/s in 00:00:00
If a rsname corrsponds to multiple variants, all of them will be imported. For example, rs111688037 can import variants NM_004638.3:c.5085T>A and NM_004638.3:c.5085T>C (chr6:31602679).
If you are interested in using a different version of dbSNP, you will need to
vtools use dbSNP-VER to download and decompress another version of dbSNP--dbfile dbSNP-VER.DB to use an alternative db file.If your database file has different fields, please edit rsname.fmt to use the correct field names.