I've used twoBitToFa: https://genome.ucsc.edu/goldenpath/help/twoBit.html

You can use bash scripting with xargs to check them in batch, otherwise I have a python snippet that calls it. You could loop through a list of variants and check them with the get_ref function below.

from subprocess import check_output
import os
import sys


class Fixer(object):

    def __init__(self):
        self.exe = "twoBitToFa"
        self.genome = "hg19.2bit"

    def get_ref(self, chromosome, start, stop):
        # Adjust coordinates from VCF input
        start_str = "-start={0}".format(str(start - 1))  # 0 based
        stop_str = "-end={0}".format(str(stop))  # Don't remove 1 here because it is [start,stop)
        chromosome_str = "-seq=chr{0}".format(chromosome)

        # Handle case where X,Y is reported as 23,24
        if chromosome_str == "-seq=chr23":
            chromosome_str = "-seq=chrX"
        elif chromosome_str == "-seq=chr24":
            chromosome_str = "-seq=chrY"

        # Run command
        output =  check_output(  [ self.exe, self.genome, 'stdout', chromosome_str, start_str, stop_str ]  )
        return "".join( output.split('\n')[1:] )