SNP value column in input snp file correspond to which information in vcf format files?

FelixKrueger / SNPsplit

Allele-specific alignment sorting

http://felixkrueger.github.io/SNPsplit/

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SNP value column in input snp file correspond to which information in vcf format files? #35

Closed brainfo closed 4 years ago

brainfo commented 4 years ago

What does the SNP value mean? Does it mean "QUAL" in vcf files or any else information?

FelixKrueger commented 4 years ago

I think originally this would indicate whether the SNP was on the top or bottom strand. I think the value is always 1 as the SNPs output by SNPsplit are always relative to the top strand, so bottom line: you can safely just ignore this column.