Tardis
Nextflow wrapper script for BilkentCompGen/tardis, runs TARDIS in QUICK MODE. See original documentation for more details.
Example Command
nextflow run lifebit-ai/Tardis
--input_folder s3://1000genomes/phase3/data/NA12878/high_coverage_alignment/NA12878.mapped.ILLUMINA.bwa.CEU.high_coverage_pcr_free.20130906.bam
--ref s3://lifebit-featured-datasets/pipelines/tardis-data/human_g1k_v37.fasta
--sonic s3://lifebit-featured-datasets/pipelines/tardis-data/human_g1k_v37.sonic
--bam_file_prefix NA12878.mapped.ILLUMINA.bwa.CEU.high_coverage_pcr_free.20130906bam_file_prefix is an optional argument to run TARDIS only on one BAM file if multiple BAMs are present in input_folder. All other arguments are mandatory.
Running on Deploit
Example can be seen by selecting "Try with example data & parameters". Substitute input_folder for your own folder containing BAM files. If the BAM was aligned against a different reference genome ref and sonic parameters will also need to be changed. Sonic files for different reference genomes can be downloaded from here or you can make your own.
Output
Output vcf files use the name of the input BAM file(s).
Example output:
