Thank you for your comment! I think what you said is the right for germline variant, but here is my vcf file example, my variant contains very low VMF/VF.(0.0740741). Does this mean somatic variant?? In FORMAT, VF is defined as "Variant UMI allele frequency, same as VMF," so I thought I have to eliminate this variant. Am I right?

##fileformat=VCFv4.2
##reference=/srv/qgen/data/genome/hg19/ucsc.hg19.fa
##FILTER=<ID=LM,Description="Low coverage (fewer than 5 barcodes)">
##FILTER=<ID=RepT,Description="Variant in tandem repeat (TFR) regions">
##FILTER=<ID=RepS,Description="Variant in simple repeats (RepeatMasker) regions">
##FILTER=<ID=HP,Description="Inside or flanked by homopolymer regions">
##FILTER=<ID=LowC,Description="Variant in Low complexity regions, as defined in RepeatMasker">
##FILTER=<ID=SL,Description="Variant in micro-satelite regions, as defined in RepeatMasker">
##FILTER=<ID=SB,Description="Strand Bias">
##FILTER=<ID=DP,Description="Too many discordant pairs">
##FILTER=<ID=MM,Description="Too many mismatches in a read. Default threshold is 6.5 per 100 bases">
##FILTER=<ID=LowQ,Description="Low base quality">
##FILTER=<ID=RBCP,Description="Variant are clustered at the end of barcode-side reads">
##FILTER=<ID=RPCP,Description="Variant are clustered at the end of primer-side reads">
##FILTER=<ID=PB,Description="Primer bias filter. odds ratio > 10 or < 0.1">
##FILTER=<ID=PrimerCP,Description="variant is clustered within 2 bases from primer sequence due to possible primer dimers">
##INFO=<ID=TYPE,Number=.,Type=String,Description="Variant type: SNP/INDEL/COMPLEX">
##INFO=<ID=RepRegion,Number=.,Type=String,Description="Repetitive region">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Total read depth">
##INFO=<ID=UMT,Number=1,Type=Integer,Description="Total used UMI depth">
##INFO=<ID=VMT,Number=.,Type=Integer,Description="Variant UMI depth">
##INFO=<ID=VMF,Number=.,Type=Float,Description="Variant UMI allele frequency">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Filtered allelic UMI depths for the ref and alt alleles">
##FORMAT=<ID=VF,Number=.,Type=Float,Description="Variant UMI allele frequency, same as VMF">


#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  20-026_S1
chr3    49693658    .   C   A   24.68   PrimerCP    TYPE=SNP;RepRegion=NA;DP=532;UMT=243;VMT=18;VMF=0.0740741;ANN=A|synonymous_variant|LOW|BSN|ENSG00000164061|transcript|ENST00000296452|protein_coding|5/12|c.6669C>A|p.Gly2223Gly|6783/15955|6669/11781|2223/3926||,A|downstream_gene_variant|MODIFIER|BSN|ENSG00000164061|transcript|ENST00000467456|retained_intron||n.*4876C>A|||||4876|  GT:AD:VF    0/1:225,18:0.0740741