-R not work in bcftools view

[biozzq]

Dear all,

I want to extract specified sites from VCF file and used following command, but it failed because many sites not in the specified sites have also been printed out. For example, the site 133089. Hope your help. Thank you very much.

bcftools-1.11/bin/bcftools view -R 18.sites --threads raw.vcf.gz -O v | grep -v "^#"
18      132827  .       C       A       5914.41 .       
18      132838  .       G       A       36067.9 .       
18      133089  .       GGACACCTGGGTGGGGGCTGGGCACCAAGACCTCACCTCTGAAGGTTAGTCCCCGAGAAAGGGCCGGGC   CGACACCTGGGTGGGGGCTGGGCACCAAGACCTCACCTCTGAAGGTTAGTCCCCGAGAAAGG
18      133137  .       G       A       226.82  . 

cat 18.sites
18      132827
18      132838
18      133137

Best wishes,
Zheng Zhuqing

[pd3]

The -R option takes into account overlapping records, this is described in the manual page. If you want to subset strictly by position, add (or replace with) the -T option.