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:
- 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
Documentation
Important Notes
- 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
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 ~]$module load VCF-kit +] Loading singularity 3.8.5-1 on cn4213 [+] Loading VCF-kit 0.2.9 ... [user@cn3316 ~]$vk -h usage: vkEnd the interactive session:[ ...] 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 ~]$