It is normal to get nothing for VAF field for INDEL
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15 months ago
A ★ 3.9k

HI

I calculated variant allele frequency for my INDELs (.vcf file) but returned empty field like below

Chrom   Position    Ref Alt TumorReadCount  TumorVariantAlleleCount TumorReferenceAlleleCount   NormalReadCount NormalVariantAlleleCount    NormalReferenceAlleleCount  VAF
chr1    9773418 AACAG   A           0           0   
chr1    19823504    T   TATATATA            0           0   
chr1    22788886    C   CA          0           0   
chr1    23511347    CGCCACCTGGTG    C           0           0   
chr1    25920544    C   CA          0           0   
chr1    27105930    T   TG

Is it normal? I mean should I expect any VAF for INDEL at all or only SNPs does have VAF? Because for SNP for the same patient I found VAF

WGS INDEL CNV • 271 views
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