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Old 01-10-2019, 06:32 AM   #2
SNPsaurus
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Location: Eugene, OR

Join Date: May 2013
Posts: 521
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You can filter your vcf for variants that fit your minor allele threshold with vcftools https://vcftools.github.io/man_latest.html

From the docs:
--non-ref-af <float>
--max-non-ref-af <float>
--non-ref-ac <integer>
--max-non-ref-ac <integer>

--non-ref-af-any <float>
--max-non-ref-af-any <float>
--non-ref-ac-any <integer>
--max-non-ref-ac-any <integer>

Include only sites with all Non-Reference (ALT) Allele Frequencies (af) or Counts (ac) within the range specified, and including the specified value. The default options require all alleles to meet the specified criteria, whereas the options appended with "any" require only one allele to meet the criteria. The Allele frequency is defined as the number of times an allele appears over all individuals at that site, divided by the total number of non-missing alleles at that site.
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