VCF format question

[NGS2009]

Do you anyone know why certain nucleotides are capitalized and some of them are lowercase in the REF/ALT fields for VCF format 4.0? Or it may be due to the results that the samtools (mpileup, bcftools) or vcfutils.pl are calling (these are tools that I used to generate the vcf file), rather than a part of the true VCF Format standard...

Thanks!!

[csoong]

perhaps your reference genome was masked