Convert a vcf file to SNP table

This is a simple tool to convert a vcf file to SNP table.



Output includes:

CHROM: chromosome
POS: position
REF: reference allele
ALT: alternative alleles (mutations compared to the reference)
QUAL: variant quality (the more reads and more counts of ALT alleles, the higher quality)
AC: “Allele count in genotypes, for each ALT allele, in the same order as listed”
AN: “Total number of alleles in called genotypes”; AN/2 = number of lines with data
DP: total reads; “Approximate read depth; some reads may have been filtered”
MQ: Mapping Quality

Then genotying data of each line: N is missing and H is heterozygous.