Hi

I have a list of chromosomes and positions that looks like this:

    1	10045
    1	93056
    1	109272
    1	127711
    1	127822
    .
    .
    .

And now I would like to use it to remove them from my vcf file. Do you know how to do this?

[bcftools][1] can do this:

    $ bcftools view -T ^list_snp_exclude.txt input.vcf > output.vf

With the `^` before the file with the coordinates one tell `bcftools` to exclude these regions.

fin swimmer


  [1]: https://www.htslib.org/doc/bcftools.html#common_options