bioinfoipec/vcftools repository overview

⁠VCFtools

This image facilitates the usage of VCFtools⁠, a program package designed for working with VCF files. The aim of VCFtools is to provide easily accessible methods for working with complex genetic variation data in the form of VCF files.

⁠Using the VCFtools image

This toolset can be used to perform the following operations on VCF files:

• Filter out specific variants.
• Compare files.
• Summarize variants.
• Convert to different file types.
• Validate and merge files.
• Create intersections and subsets of variants.

Frequently used tools in this suite are⁠:

• vcf-annotate
• vcf-compare
• vcf-concat
• vcf-consensus
• vcf-contrast
• vcf-convert
• vcf-fix-newlines
• vcf-fix-ploidy
• vcf-indel-stats
• vcf-isec
• vcf-merge
• vcf-phased-join
• vcf-query
• vcf-shuffle-cols
• vcf-sort
• vcf-stats
• vcf-subset
• vcf-to-tab
• vcf-tstv
• vcf-validator
• vcftools

To obtain the help of an application, you just need to run: docker run --rm bioinfoipec/vcftools <vcftools-application-name> --help (e.g. docker run --rm bioinfoipec/vcftools vcftools --help)

⁠Using the VCFtools image in Linux

To run a package, you should adapt and run the following command: docker run --rm -v /your/data/dir:/data bioinfoipec/vcftools <vcftools-application-name> <options>

In this command, you should replace:

• /your/data/dir to point to the directory that contains the input files you want to analyze.
• <vcftools-application-name> to the name of the VCFtools application you want to use.
• <options> with the specific options of the VCFtools application. These options will include the input/output files, which should be referenced under /data/.

For instance, to output a new VCF file from the input VCF file that removes any indel sites, you should run: docker run --rm -v /your/data/dir:/data bioinfoipec/vcftools vcftools --gzvcf /data/ALL.chrY.phase3_integrated_v2a.20130502.genotypes.vcf.gz --remove-indels --recode --recode-INFO-all --out /data/output

⁠Test data

To test the previous command, the dataset used is available here⁠.