Using¶

WOLAND has three main scripts: woland-anno.pl, woland-report.pl and woland-batch.pl) plus a acessory script woland-bed.pl. Please observe descriptions of each script, input file file requirements, usage and outputs.

Scripts¶

woland-batch.pl¶

Script which automatically runs multiple instances of woland-anno.pl and build a single report using woland-report.pl:

$ perl woland-batch.pl <input_table> <chr_profile> <hs_window> <genome_version>

woland-anno.pl¶

Script used to calculate mutational patterns of a single annotated variant file. Uses a single <variant_function> to calculate all patterns in a single result folder for <results-variant_function> provided:

$ perl woland-anno.pl <variant_function> <chr_profile> <hs_window> <genome_version>

woland-report.pl¶

Script used to build a report of multiple annotated variant files assigned as groups with results already done by woland-anno.pl:

$ perl woland-report.pl <input_table>

Inputs¶

<input.table>¶

Regular tabular file without header. First column is group name. Second column is file sample name of annovar annotated.variant file. Samples files MUST be located in the Woland install folder.

<annovar.variant_function>¶

Annotated .variant_function file which can be obtained using annotate-variation.pl script from ANNOVAR.

<chromosome_profile>¶

Regular tabular file without header . First column is chromosome name in chr format (e.g. chr13). Second column is chromosome length sequenced. User can build this file with target .BED file using woland-bed-to-profile.pl.

<hotspot_window>¶

A natural number N (N>1), for hotspot window length. Hotspot window corresponds to N nucleotides flanking each SNV.

<genome_version>¶

Genome version of genomes/genome_<genome_version> and genomes/refseq_<genome_version> files.

<coordinates.bed>¶

Coordinates of target regions used in sequencing experiment in BED format.

Usage¶

woland-batch.pl¶

woland.batch enables batch submission of multiple samples as provided by <input.table> file. This script runs Woland-anno.pl for each sample followed by Woland-report.pl generating one result folder for each sample file provided and a grouped report folder for whole analysis as provided by <input.table>

$ perl woland-batch.pl <input.table> <chromosome_profile> <hotspot_window> <genome_version>

woland-anno.pl¶

Uses a single <annovar.variant_function> to calculate all patterns in a single result folder for <annovar.variant_function> provided:

$ perl woland-anno.pl <annovar.variant_function> <chromosome_profile> <hotspot_window> <genome_version>

woland-report.pl¶

This script uses a group of samples to perform Woland-anno.pl script for each sample provided to build an unique grouped report output folder for the analysis. Sample names and groups are provided by <input.table> and one result folder is also generated for each sample provided:

$ perl woland-report.pl <input.table> <chromosome_profile> <hotspot_window> <genome_version>

woland-bed.pl¶

This script generates a <chromosome_profile> file using a .bed file from a targeted-sequencing experiment, for example. The <chromosome_profile> file could be used in other Woland scripts:

$ perl woland-bed.pl <coordinates.bed>