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!!
Thanks!!
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