SVAltAlign Queue script

Geraldine_VdAuwera

1. Introduction

SVAltAlign.q is a sample Queue script that is part of Genome STRiP.

This script realigned previously unmapped reads against putative alternate
alleles generated from a VCF file describing a set of variants to be
genotypes. The output is a merged bam file that contains these alignements to
the alternate alleles. These alterante allele alignments are then used as
input to genotyping.

2. Inputs / Arguments

• -vcf <input-vcf-file> : A VCF file containing descriptions of the
  structural variations. : Only records for structural variations with precise
  breakpoints will be processed.

• -I <bam-file> : The set of input BAM files containing records to realign.

• -md <directory> : The metadata directory containing metadata about the
  input data set.

• -R <fasta-file> : Reference sequence. : An indexed fasta file containing
  the reference sequence. The fasta file must be indexed with samtools faidx
  or the equivalent.

• -altAlleleFlankLength <n> : The length of flanking sequence from the
  reference genome used during realignment (default 200).

• -alignUnmappedMates <boolean> : Whether to align unmapped mates of mapped
  reads to the alternate alleles (default true). : If false, then unmapped reads
  with a POS field will not be ignored.

• -configFile <configuration-file> : This file contains values for
  specialized settings that do not normally need to be changed. : A default
  configuration file is provided in conf/genstrip_parameters.txt.

3. Outputs

• -O <bam-file> : The default output for this pipeline is a single merged
  bam file for all input bam files and all alternate alleles. : The sequence
  identifier for an alternate allele is VariantID_N where N is the index of the
  alternate allele in the VCF file (i.e. the first alternate allele is allele
  1).

4. Running

The SVAltAlign.q script is run through Queue.

Because Genome STRiP is a third-party GATK library, the Queue command line
must be invoked explicitly, as shown in the example below.

java -Xmx2g -cp Queue.jar:SVToolkit.jar:GenomeAnalysisTK.jar \
    org.broadinstitute.sting.queue.QCommandLine \ 
    -S SVAltAlign.q \ 
    -S SVQScript.q \ 
    -gatk GenomeAnalysisTK.jar \ 
    -cp SVToolkit.jar:GenomeAnalysisTK.jar \
    -configFile /path/to/svtoolkit/conf/genstrip_parameters.txt \ 
    -tempDir /path/to/tmp/dir \ 
    -md metadata \ 
    -R Homo_sapiens_assembly18.fasta \ 
    -vcf input.vcf \ 
    -I input1.bam -I input2.bam \ 
    -O output.bam \ 
    -run \ 
    -bsub \
    -jobQueue gsa \ 
    -jobProject 1KG \ 
    -jobLogDir logs 

5. Typical Queue Arguments

Queue typically requires the following arguments to run Genome STRiP
pipelines.

• -run : Actually run the pipeline (default is to do a dry run).

• -S <queue-script> : Script to run. : The base script SVQScript.q from the
  SVToolkit should also be specified with a separate -S argument.

• -gatk <jar-file> : The path to the GATK jar file.

• -cp <classpath> : The java classpath to use for pipeline commands. This
  must include SVToolkit.jar and GenomeAnalysisTK.jar. : Note: Both -cp
  arguments are required in the example command. The first -cp argument is for
  the invocation of Queue itself, the second -cp argument is for the invocation
  of pipeline processes that will be run by Queue.

• -tempDir <directory> : Path to a directory to use for temporary files.

6. Queue LSF Arguments

• -bsub : Use LSF to submit jobs.

• -jobQueue <queue-name> : LSF queue to use.

• -jobProject <project-name> : LSF project to use for accounting.

• -jobLogDir <directory> : Directory for LSF log files.