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Variants annotation
===================
The script "snpEffAnnotate.py" is designed for variant annotation and effect
prediction for variants found by C-Sibelia. It can be launched without
arguments from directory with C-Sibelia results:
snpEffAnnotate.py
If you want to specify your own vcf file as input for this tool, type:
snpEffAnnotate.py -i variants.vcf
By default, all outup files are located in './annotation' directory, name of
annotated vcf is variant_ann.vcf. You can specify other directory with the "-o"
option, if specified directory is not exists it will be created. For example:
snpEffAnnotate.py -i variants.vcf -o annotation
Description of output file format can be found at
http://snpeff.sourceforge.net/SnpEff_manual.html#output
Take into account, that by default, script uses ##assembly field from vcf file
to get NCBI database name. For example, a possible value of this field can be
"##assembly=gi|57116681|ref|NC_000962.2|".
One more important note about vcf is that #CHROM column must contain cromosome
name exactly the same as in snpEff database. For assembly name above it will be
"NC_000962".
If you wish, you can specify snpEff database name with the "--db" argument.
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