Biowulf High Performance Computing at the NIH
VCF-kit: assorted utilities for the variant call format

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:

Documentation
Important Notes

Interactive job
Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.

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

[user@biowulf]$ sinteractive --mem=4g 
[user@cn3316 ~]$module load VCF-kit
[user@cn3316 ~]$git clone https://github.com/AndersenLab/VCF-kit.git
[user@cn3316 ~]$vk -h
[+] Loading bwa 0.7.17 on cn2367
[+] Loading samtools 1.10  ...
[+] Loading samtools 1.9  ...
[+] Loading blast 2.5.0+  ...
[+] Loading muscle  3.8.31
[+] Loading VCF-kit 0.2.8  ...
[user@cn3316 ~]$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 ~]$vk calc genotypes $VK_DATA/test.vcf.gz 
n       ref     het     alt     mis
937     14      0       0       0
327     13      0       0       1
243     13      0       1       0
168     12      0       0       2
101     11      0       0       3
93      12      0       1       1
90      12      0       2       0
73      10      0       0       4
63      11      0       3       0
47      10      0       4       0
37      11      0       1       2
36      9       0       0       5
36      8       0       0       6
32      11      0       2       1
31      10      0       1       3
28      10      0       3       1
28      9       0       4       1
25      10      0       2       2
23      13      1       0       0
21      9       0       5       0
20      7       0       0       7
19      9       0       1       4
19      8       0       1       5
17      8       0       6       0
15      11      1       0       2
15      6       0       0       8
13      9       0       2       3
13      9       0       3       2
...
1       7       5       2       0
1       3       3       1       7
1       8       4       2       0
1       0       0       12      2
[user@cn3316 ~]$vk calc genotypes $VK_DATA/QX1211.indels.vcf.gz 
n       ref     het     alt     mis
74493   0       0       1       0
8567    0       1       0       0
End the interactive session:
[user@cnR3316 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$