Uses bcftools view to filter down variants in a VCF using a bed file. Uses dockerised bcftools v1.13.
Separates the variant calling and bed restriction steps (previously bed restriction was applied by GATK in the pipelines). This means the entire pipeline will not need to be re-run if a different BED file is required.
The required input files are as follows:
| File | Pattern | Info |
|---|---|---|
| vcf | *.vcf.gz | A vcf file containing variants from vcf that fall within the regions given in the bed file |
| vcf index file | *.vcf.gz.tbi | The index file of the vcf file to be filtered |
| bed file | *.bed | Optional. The bedfile you wish to use to filter the vcf file with. If not provided the app will exit without filtering, producing no output |
- Zipped VCF file (*.vcf.gz) - contains variants from vcf that fall within the regions given in the bed file.
- Test if a BED file was provided - if not provided does not continue.
- The app downloads the input files
- Loads the bcftools docker image from the .tar.gz file
- Runs the bcftools command. -R supplies a file containing regions to restrict the input file on. Returns all
positions overlapping the regions specified in the bed file. Therefore indels that cover both inside and outside a
region are returned.
bcftools view input_vcf##idx##input_vcf_index -R bedfile.bed -O z -o $input_vcf_prefix.vcf.gz - The bcftools output .vcf.gz file is uploaded to DNAnexus.
- The project which the app is run on must be shared with the user mokaguys
The bcftools docker image was created using the Dockerfile, tagged, and saved as a bcftools.tar.gz file, saved in the 001_ToolsReferenceData project. The app loads the docker image from the .tar.gz file each time it is run.
sudo docker build - < Dockerfile
sudo docker tag <image_id> samtools/bcftools:1.13
sudo docker save samtools/bcftools:1.13 | gzip > bcftools_v1.13.tar.gz
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