Vcall

A variantcalling pipeline.

How to run it

1. Have Docker installed
2. Open Command Prompt
3. In Command Prompt type:

docker pull jpmatos/vcall:0.2.2 (or other tag)

4. Config the config_docker.yaml by changing 'Dir_settings:', 'Settings:' and 'Threads':
5. In Command Prompt type:

docker run -v </your_directory/>:/mnt/share jpmatos/vcall:0.2.2 snakemake --snakefile /mnt/share/vcall-pipe.snake -p /mnt/share/repo/example_dataset/output/<analisis_to_make> --cores <n_of_avaliable_cores>

| Analisis_to_make:

For comparation between Tumor and Normal reads:

/{your_read}.Normal_VS_Tumor_output.vcf 

For Analisis of Copy-number variantes:

/{your_read}.my_reference.cnn

For Annotation:

/{your_read}.exome_seq_final.vcf.gz

6. Then collect your output-file:

Output dir example:
/mnt/share/repo/example_dataset/output/T.vcf

Some suggestions:

• If your docker is slow, try this:

Open docker container:

docker run -v </your_directory/docker_folder>:/mnt/share/ jpmatos/vcall:0.2.2

Then type:

snakemake --snakefile /mnt/share/vcall-pipe.snake -p /mnt/share/repo/example_dataset/output/<your_read>.Normal_VS_Tumor_output.vcf --cores <n_of_avaliable_cores>

This time the container will not close after the pipeline run.