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.
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