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INSTALL.md

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Installation

External software

*tested versions indicated, may not be the most recent version. For BBT, v3.0.0b is required.

External files

To run PAVFinder, the following reference sequence and annotation files are required:

  • genome FASTA and index files

  • For example, to prepare hg19 files from UCSC:

    wget ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/chromosomes/chr*.fa.gz
zcat chr*.fa.gz > hg19.fa && rm chr*.fa.gz
samtools faidx hg19.fa
bwa index hg19.fa
gmap_build -D . -d hg19 hg19.fa

  • annotation VCF and index files

  • For example, to prepare Refseq genes from UCSC:

    wget http://hgdownload.cse.ucsc.edu/goldenpath/hg19/database/refGene.txt.gz
zcat refGene.txt.gz | cut -f2- | ~rchiu/bin/genePredToGtf file stdin refGene.gtf
sort -k1,1 -k4,4n refGene.gtf > refGene.sorted.gtf
bgzip refGene.sorted.gtf
tabix -p gff refGene.sorted.gtf.gz

  • transcriptome FASTA and index files

  • To create a reference transcriptome FASTA, PAVFinder provides a utility for making it (available under 'bin' for pip virtualenv install)

    extract_transcript_sequence.py <gtf> <fasta_output> <genome_fasta> --index

    A transcript FASTA and a corresponding BWA index will be genearated

If running TAP, after installation of PVT(below) full paths of the above reference and annotation files can be specified in /path/to/virtualenv/config/tap.cfg which can be passed to TAP via --params

genome_index = /real/path/to/gmapdb hg19
transcripts_fasta = /real/path/to/transcripts.fa
genome_fasta = /real/path/to/genome.fa
gtf = /real/path/to/gtf
suppl_annot = /real/path/to/supplementary_gtf (optional)

Installing the Python PVT package

  1. pip install virtualenv
  2. virtualenv <DIR>
  3. source <DIR>/bin/activate
  4. pip install -U cython
  5. pip install git+https://github.com/BirolLab/pavfinder_transcriptome.git#egg=pavfinder_transcriptome

After successful installation, the following will be available in different sub-directories under the virtualenv directory:

  1. Python scripts for detecting structural (find_sv.py) and splice (map_splice.py) variants, and the TAP pipeline script (tap.py) will be in "bin"
  2. A template config file (tap.cfg) for running TAP will be in "config"
  3. Sample data will be in "test"