created the VarTable options list

OPTIONS.md

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+## VarTable Options
+
+
+
+Usage
+---------
+
+    $ vartable_report --input-vcf [../filename.vcf] --type [basecaller] \
+		--input-bam [../filename.bam] --input-ref [../filename.fasta] \
+		--minpercent [20] --minbq [25] --mindepth [10] \
+		--output-err [filename.err] --input-prm [../filename.fasta] \
+		--output-name [filename.tsv] --input-region [10 200] \
+		--stats
+
+## (Required)
+**--input-vcf**		input VCF file
+
+**--type**		input flag (base_caller | lofreq), this differentiates b/t a VCF with all positions and VCF with only variant positions
+
+**--input-bam**		input BAM file
+
+**--input-ref**		input reference FASTA file or GenBank, gb extension file (this will parse for annotated information)
+
+**--minpercent**	input variant call percentage, for example 20%, 5% or 1%
+
+**--minbq**		input minimum base nt quality, for example 25% or 30%
+
+**--mindepth**		input minimum depth of coverage for each nt base, for example 10
+
+**--output-err**	input name of output file for user troubleshooting or submit the error file for help
+
+## (Optional)
+**--input-prm**		input primer FASTA file
+
+**--output-name**	input the desired output filename (default format: tsv)
+
+**--input-region**	input start and end positions; variant table will isolate variants within that region
+
+**--stats**		outputs a file containing genome statistics