Input: The expected input is a vcf file with a minimum of 5 tab-separated columns required: CHROM POS ID REF ALT. Additional
columns are ignored. Header lines starting with # are ignored. CHROM should be written as 1,2,3 ... 22,X,Y. Multiple ALT
can be supplied comma-separated - the variant entry is cloned and a REF ALT sequence pair extracted for every ALT. Indels are
skipped at the moment but should be written with a dot. (See: example input data, VCFv4.0 format) Output: Two .txt files - one containing successfully converted variants and a second containing failed or skipped variants with explanation.
The vcf_to_sasq accessory tool expects input data in VCFv4.0 format.