How to filter Germline variants from vcf file?

Question

[leukippus0116]

Hello. I'm new to Bioinformatics working on NGS data. Now I'm working on detecting SNP variants causing multiple sclerosis.

I selected some genes for target resequencing and got NGS data. I put these datas into Qiagen's NGS variant calling pipeline and got vcf files for each samples.

I checked them and realized that these vcf files contain very low variant minor allele frequency(VMF) SNPs. I want to deal with germline variants, so I'm trying to filter these low VMF variants.

I'm using vcftools but I can't solve this problem... I know I have to study more but time is running out so is there any kind person who could help me please...? Thank you.

[Ram]

If you have per-sample VCFs, the only possible minor AF values for bi-allelic variant loci are 0.5 and 1. What do you mean by "very low minor allele frequency"?

[leukippus0116]

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

[Ram]

You did not mention UMIs at all in your initial post - I think UMIs are only involved in single cell sequencing, and I don't really know single cell technologies. Maybe experts on the technology can chime in.