I have population SNP data in VCF format, and I found that some SNPs have a great similarity across samples(> 99%). For example:
CHROM_POS s0 s1 s2 s3 s4 s5 s6 s7 s8 s9 chr1_1 A G G A G G A A G A chr1_2 A G G A G G A A G T chr1_3 C C C A C A C C C C
The similarity between chr1_1 and chr1_2 is 0.9, because they have a different SNP in sample s9.
Is there a good way to remove these similar SNPs before I put the data into another pipeline?
Added: These SNPs will be used for GWAS analysis.