VCF-kit is a collection of utility tools for processing and analyzing the VCF (variant call format) files, including primer generation for variant validation, dendrogram production,genotype imputation from sequence data in linkage studies, and additional tools to be used by statistical and population geneticists.

References:

• Daniel E. Cook and Erik C. Andersen
  VCF-kit: assorted utilities for the variant call format
  Bioinformatics 2017, 33(10), 1581–1582. doi: 10.1093/bioinformatics/btx011

• VCF-kit home page

• Module Name: VCF-kit (see the modules page for more information)
• Unusual environment variables set
  • VK_HOME  VCF-kit installation directory
  • VK_BIN       VCF-kit executable directory
  • VK_DOC       VCF-kit documentation directory
  • VK_DATA    VCF-kit test data directory
  • VK_SRC    VCF-kit source code directory

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive --mem=4g 
[user@cn3316 ~]$module load VCF-kit
+] Loading singularity  3.8.5-1  on cn4213
[+] Loading VCF-kit 0.2.9  ...
[user@cn3316 ~]$vk -h
usage:
  vk  [...]
  vk setup
  vk -h | --help
  vk --version

commands:
  calc
  call
  filter
  geno
  genome
  hmm
  phylo
  primer
  rename
  tajima
  vcf2tsv
[user@cn3316 ~]$vk calc -h
usage:
  vk calc sample_hom_gt 
  vk calc genotypes [--frequency] 
  vk calc spectrum 

Example

options:
  -h --help                   Show this screen.
  --version                   Show version.
[user@cn3316 ~]$cp $VK_DATA/* . 
[user@cn3316 ~]$vk calc genotypes test.vcf.gz 
n       ref     het     alt     mis
937     14      0       0       0
327     13      0       0       1
243     13      0       1       0
168     12      0       0       2
101     11      0       0       3
93      12      0       1       1
90      12      0       2       0
73      10      0       0       4
63      11      0       3       0
47      10      0       4       0
37      11      0       1       2
36      9       0       0       5
36      8       0       0       6
32      11      0       2       1
31      10      0       1       3
28      10      0       3       1
28      9       0       4       1
25      10      0       2       2
23      13      1       0       0
21      9       0       5       0
20      7       0       0       7
19      9       0       1       4
19      8       0       1       5
17      8       0       6       0
15      11      1       0       2
15      6       0       0       8
13      9       0       2       3
13      9       0       3       2
...
1       7       5       2       0
1       3       3       1       7
1       8       4       2       0
1       0       0       12      2
[user@cn3316 ~]$vk calc genotypes QX1211.indels.vcf.gz 
n       ref     het     alt     mis
74493   0       0       1       0
8567    0       1       0       0

[user@cnR3316 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$