mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
Saket Choudhary
5eef793e8c
an integer for VCF4.1 files. I am not sure if there are better ways or beter checks that can be implemented to do this. So, this should require discussions. The description of ##INFO and ##FORMAT tag as given on [http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41] is : ##INFO=<ID=ID,Number=number,Type=type,Description=”description”> Possible Types for INFO fields are: Integer, Float, Flag, Character, and String. The Number entry is an Integer that describes the number of values that can be included with the INFO field. For example, if the INFO field contains a single number, then this value should be 1; if the INFO field describes a pair of numbers, then this value should be 2 and so on. If the field has one value per alternate allele then this value should be 'A'; if the field has one value for each possible genotype (more relevant to the FORMAT tags) then this value should be 'G'. If the number of possible values varies, is unknown, or is unbounded, then this value should be '.'. The 'Flag' type indicates that the INFO field does not contain a Value entry, and hence the Number should be 0 in this case. The Description value must be surrounded by double-quotes. Double-quote character can be escaped with backslash (\") and backslash as \\.