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  • NGS2009
    Junior Member
    • Dec 2009
    • 4
    #1

    VCF format question

    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!!
    Tags: None
    • csoong
      Member
      • Jun 2009
      • 74
      #2
      perhaps your reference genome was masked

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