Accessory Tools - vcf_to_sasq


Convert vcf format to Sasquatch input format

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.





(VCFv4.0 format - see example)

Alternatively, upload a vcf file