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.