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bamsurgeon-nf

in-silico simulations of mutations using bamsurgeon

Summary

This nextflow script executes two major steps: * variant simulation using the script generate_varfiles.r, variant allelic fractions are randomly distributed (in log scale) * in-silico intoduction of these variants in BAM files * caution: for the moment, this requires two technical replicates of the same sample (used to boost the precision of the variant calling)

Dependencies

Please make sure that the following tools are installed on your system and are in your PATH:

• bamsurgeon addsnv.py and addindels.py executable files. Note that you will need to use Python 2.7 by default.

• nextflow

  curl -fsSL get.nextflow.io | bash
  

  To move it to a location in your $PATH (/usr/local/bin for example here):

  sudo mv nextflow /usr/local/bin
  

• R software (tested with R version 3.2.3)

Execution

Nextflow seamlessly integrates with GitHub hosted code repositories:

nextflow run iarcbioinfo/bamsurgeon-nf  --bam_folder BAM/ --genomeRef hg19.fasta --picardpath picard.jar --bed positions.bed --n_mutations 10 --hotspot_size 2

This command will generate 10 random mutations from your bed file (with coverage control, i.e. a mutation is introduced only if the number of mutated reads would be higher than the threshold at 5) on 2 technical replicates of a sample present in your BAM folder, with allelic fraction following a logarithmic random distribution (see this script: generate_varfiles.r, caution: this process used for the moment 10 CPUs).

Then these mutations will be added to your BAM files using bamsurgeon. If one of the mutation you want to add did not succeed, a file *failed.var will be present on your $outputFolder/mut_bam directory containing this mutation.
You can use your own variant files, by providing --varFolder option.

The tool can also deal with indels, by provinding --del or --ins option in addition to --indel_size mysize one.

Help section

You can print the help manual by providing --help in the execution command line:

nextflow run iarcbioinfo/bamsurgeon-nf --help