search

FOI-Bioinformatics / CanSNPer2

CanSNPer2: A toolkit for SNP-typing bacterial genomes.
GNU General Public License v3.0
6 stars 2 forks source link

format of --annotation snp input #22

Open CarolineOhrman opened 4 years ago

CarolineOhrman commented 4 years ago

It would be convenient to be able to comment out lines in the snp file used as input for building the database and also to have a commentfield.

Proposed format

snp_id  strain  reference   genome  position    derived_base    ancestral_base  comment
B.1 francisella Birdsell2014    OSU18   1710718 T   C   this is an optional free text comment field
B.2 francisella Vogler2009  OSU18   19938   T   G
B.3 francisella Vogler2009  OSU18   1540403 T   C
#B4 is one of the major branches
B.4 francisella Vogler2009  OSU18   1350634 A   T   position in SCHUS4 XXXX
B.5 francisella Vogler2009  OSU18   84943   T   C
#B6 is one of the major branches
B.6 francisella Vogler2009  OSU18   1471420 T   C
...