Simulate in-silico variants for a trio

Input:

• 3 bam files with the alignment of parents and offspring [e.g. NA12878 NA12891 NA12892]
• 1 vcf file for the trio
• 1 txt file with the variants to simulate
  • Each variants has a field which needs to be one of the following values for inheritance:
    • Recessive
    • DeNovo
    • Compound

Output:

• simulated reads
• simulated vcf file : simulated.vcf
• combined vcf file appending and sorting the simulated.vcf to the family.vcf: [family_file]_simulated_variant.vcf

Availability:

• Code and examples are available here:

Requirements:

• samtools
• vcf-sort
• python modules: sys, os, subprocess, argparse, random, numpy

Usage:

python variant_simulator.py \ --mat_bam mother.bam
--pat_bam father.bam
--affected_bam offspring.bam
--fam_vcf [family_file].vcf \ --varfile [variants to si`mulate].txt