vcffixup

       Erik Garrison and vcflib contributors.

vcffixup (vcflib)                                                                                    VCFFIXUP(1)

       Generates a VCF stream where AC and NS have been generated for each record using sample genotypes

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       Copyright  2011-2024  (C)  Erik Garrison and vcflib contributors.  MIT licensed.  Copyright 2020-2024 (C)
       Pjotr Prins.

vcffixup

              Count the allele frequencies across alleles present in each record in the VCF file. (Similar to vcftools --freq.)

              Uses genotypes from the VCF file to correct AC (alternate allele count), AF
              (alternate allele frequency), NS (number of called), in the VCF records.  For
              example:

                  % vcfkeepsamples file.vcf NA12878 | **vcffixup** - | vcffilter -f "AC > 0"

              Would downsample file.vcf to only NA12878, removing sites for which the sample
              was not called as polymorphic.

              Type: transformation

vcflib(1)

vcffixup