After merging my vcf file containing specific variants with those variants in 1000 genome vcf, the ID column of merged VCF file is like below:
which only the rs60323161;chr1:39244787:SG are common variants. Please kindly let me know how can keep only common variants in the merged vcf file?
bcftools view -T for keeping just common variants, but it didn't work well; actually, the variants like below is still exist in the file, which chr1:39448418:SG should be removed
I also tested
grep -Fwvf and
grep -vf for removing those variants, but none of them works well. Please kindly share me your solution?