INPUT
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FunSEQ takes BED or VCF files as input 
* Please prepare your input in hg19 *


1. BED format 
In addition to the three required BED fields, please prepare your file as follows (5 required fields, tab-delimited): 
chrom	chromStart	chromEnd	Reference.allele	Alterative.allele	... 
* chrom - The name of the chromosome (e.g. chr3, chrY). 
* chromStart - The starting position of the feature in the chromosome. The first base in a chromosome is numbered 0.
* chromEnd - The ending position of the feature in the chromosome. The chromEnd base is not included in the display of the feature. 
For example, position 100 (1-based coordinate) in chromosome 1 is defined as "chr1 99 100", corresponding to position 99 in 0-based coordinate. 
* Reference.allele - The reference allele of SNVs
* Alternative.allele - The alternative allele of SNVs. 

eg. To run the program properly, please strictly follow the format. Tab delimited.

chr1  213941196  213941197	G	T	...
chr1  213942363  213942364	A	C	...
chr1  213943530  213943531	T	A	...


2. VCF format 
The header line names the 8 fixed, mandatory columns. These columns are as follows (tab-delimited): 
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO 

eg. To run the program properly, please strictly follow the format. Tab delimited.

##fileformat=VCFv4.0
#CHROM POS    ID        REF  ALT     QUAL FILTER INFO ...
2      4370   rs6057    G    A       29   .      ...   ...