This is a SnakeMake pipeline based on RetroSeq https://github.com/tk2/RetroSeq, a tool for discovery of transposable element variants. The pipeline runs RetroSeq configured to seach for HERV-K insertions, filters RetroSeq predictions and verifies the insertions by assembling the regions around each insertion and running the assembled contigs through RepeatMasker.

open config.yaml file and update all directories: e.g. CRAM or BAM file path; output directory path; RepeatMasker path;

If you already have a reference genome (and it is indexed), update the path to it in config.yaml If you do not, run the script downloadHG19.sh in order to install it and index it.

bash downloadHG19.sh PATH_TO_DIR_TO_PLACE_REFERENCE_GENOME

update the path to the newly added and indexed human genome in config.yaml

``

https://github.com/rmhubley/RepeatMasker RepeatMasker is needed for the verification step. Without it you can still run RetroSeq and filter the insertions.

Important: After the installation of RepeatMasker, update the installation path in the config.yaml file.

Once the paths in config.yaml point to CRAM/BAM path, path to the reference genome and the output path - you can run the pipeline on the provided sample.bam in order to predict insertions, filter them and split them in known and novel.

If the SAMPLES variable in Snakefile is updated to contain a list of samples, you can run it like this, for cores use the number of samples that can be run in parallel:

snakemake --use-conda --use-envmodules --cores 20

or to run on a single file:

snakemake --use-conda --use-envmodules --cores 1 <MY_OUTPUT_DIRECTORY>{/filter/sample.bed,/confirmed/sample.retroseqHitsConfirmed.bed}