1% VCFFIXUP(1) vcffixup (vcflib) | vcffixup (VCF transformation) 2% Erik Garrison and vcflib contributors 3 4# NAME 5 6**vcffixup** 7 8# SYNOPSIS 9 10**vcffixup** <vcf file> 11 12# DESCRIPTION 13 14Generates a VCF stream where AC and NS have been generated for each record using sample genotypes 15 16 17 18# OPTIONS 19 20``` 21 22 23 24 25Count the allele frequencies across alleles present in each record in the VCF file. (Similar to vcftools --freq.) 26 27Uses genotypes from the VCF file to correct AC (alternate allele count), AF 28(alternate allele frequency), NS (number of called), in the VCF records. For 29example: 30 31 % vcfkeepsamples file.vcf NA12878 | **vcffixup** - | vcffilter -f "AC > 0" 32 33Would downsample file.vcf to only NA12878, removing sites for which the sample 34was not called as polymorphic. 35 36Type: transformation 37 38``` 39 40 41 42 43 44# EXIT VALUES 45 46**0** 47: Success 48 49**not 0** 50: Failure 51 52# SEE ALSO 53 54 55 56[vcflib](./vcflib.md)(1) 57 58 59 60# OTHER 61 62## Source code 63 64[vcffixup.cpp](https://github.com/vcflib/vcflib/blob/master/src/vcffixup.cpp) 65 66# LICENSE 67 68Copyright 2011-2020 (C) Erik Garrison and vcflib contributors. MIT licensed. 69 70<!-- 71 Created with ./scripts/bin2md.rb scripts/bin2md-template.erb 72--> 73