# Weaver

## Allele-Specific Quantification of Structural Variations in Cancer Genomes

Version 0.20

Bamtools libraries are needed, included in Weaver_SV/lib and Weaver_SV/inc

Parallel::ForkManager perl package is needed

Bedtools

Samtools

BOOST C++ library

BWA

Bowtie

export LD_LIBRARY_PATH=<PREFIX>/Weaver/Weaver_SV/lib/:$LD_LIBRARY_PATH

libz required //-lz flag

1 Modify the required BOOST directory in src/Makefile

2 ./INSTALL.sh

wget http://bioen-compbio.bioen.illinois.edu/weaver/Weaver_data.tar.gz

EXAMPLE DATA =========

wget http://bioen-compbio.bioen.illinois.edu/weaver/Weaver_example.tar.gz

Weaver PLOIDY -f SIMU.fa -S FINAL_SV -s SNP -g REGION -w X.bam.wig -r 0 -m map100mer.bd -p 64 solo_ploidy TARGET 2 Weaver LITE -f SIMU.fa -S FINAL_SV -s SNP -g REGION -w X.bam.wig -r 0 -m map100mer.bd -p 64 -t 20 -n 0

SV finding

• Input: BAM file from BWA
• Output: VCF file for SV

Master program to generate SV together with other inputs needed for Weaver

• Input: 1000 Genomes Project Phase 1 haplotypes

Core MRF program

• Input: SV

• Outputs:

  1. Purity and haploid-level sequencing coverage
  2. Allele specific copy number of genomic regions
  3. Allele specific copy number of structural variations
  4. Relative timing of structural variations
  5. Cancer scaffolds
  6. Phasing of germline SNPs in CNV regions

Core MRF program, with SNP phasing disabled to speed up

• Inputs:

  1. SV
  2. reference
  3. Mappability (available for hg19)
  4. Region (available for hg19)
  5. wig (from bam)

Weaver PLOIDY -f -S -s ../SNP_dens -g GAP_20140416_num -w -r 1 -m -p 16

• Inputs:

  • -f reference file (fasta), should match the reference used in original bam file. Especially for most TCGA datasets, the alignment was performed on //www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta, which does not have "chr" prefix [MANDATORY]
  • -S SV file, with format consistent with Weaver_SV. [MANDATORY]
  • -s SNP file, with ref and alt mappings [MANDATORY]
  • -w wig file from bam, storing the coverage information [MANDATORY]
  • -r 1, if first time running (generating temp files); 0 if want to use existing temp files. [default 1]
  • -m mappability file, download from http://bioen-compbio.bioen.illinois.edu/weaver/Weaver_data.tar.gz [MANDATORY]
  • -p number of cores [default 1]

Wiggle file need to be declared with fixedStep, step 1 and span 1 fixedStep chrom=chr1 start=9994 step=1 span=1 if a chromosome has multiple declaration lines, they need to be sorted based on position: fixedStep chrom=chr1 start=9994 step=1 span=1 X X X fixedStep chrom=chr1 start=100 step=1 span=1 X X X Is not allowed

Must be sorted and indexed.

SNP file:

NGS SNP link file

1KGP SNP link

Genome region file:

GAP regions in assembly are annotated.

Storing phased allele specific copy number of genome

CHR BEGIN END ALLELE_1_CN ALLELE_2_CN

Structural variation copy number and phasing, catagory

CHR_1 POS_1 ORI_1 ALLELE CHR_2 POS_2 ORI_2 ALLELE CN germline/somatic_post_aneuploidy/somatic_pre_aneuploidy

Yang Li Jian Ma's Computational Genomics Lab at Carnegie Mellon The code was developed by Yang Li when the Ma lab was at the University of Illinois at Urbana-Champaign

https://github.com/ma-compbio/Weaver