ReferenceBundel¶

Constructing a custom reference metadata bundle
see http://www.broadinstitute.org/software/genomestrip/node_ReferenceMetadata.html

1. reference.fasta : the genome file in fasta format (and associated .fai index file)
   provided by the user
2. reference.fasta.length : ...
   computed using fastalength
3. reference.ploidymap : expected ploidy of the different chromosomal regions
   provided by the user
4. reference.gendermask.bed : regions with unreliable read depth on human sex chromosomes (eg. pseudoautosomal regions)
   provided by the user
5. reference.svmask.fasta : genome alignability mask (in indexed fasta format) that is used to deterimine whether reference sequence should be considered to be uniquely alignable
   computed using ComputeGenomeMask from gatk :
   

   java -cp ${classpath} -Xmx4g org.broadinstitute.sv.apps.ComputeGenomeMask
       -R ${reference} -O svmask_${chr}.fasta -readLength ${readLength}  
       -sequence ${chr}
   

   
   putting everything back into a single file and indexing (see also README_GenomeSTRIPreferenceBundle)
6. reference.rdmask.bed : bed file specifying a set of regions to use for overall sequencing depth estimation
   keeping only autosomes
7. reference.gcmask.fasta : genome mask (in indexed fasta format) that is used for gc-bias estimation in each sequencing library
   removing sex chromosomes and repeats (see README_GenomeSTRIPreferenceBundle)
8. reference.lcmask.fasta : genome mask (in indexed fasta format) that masks low-complexity sequence and is used in read-depth analysis
   removing simple repeats (see README_GenomeSTRIPreferenceBundle)
9. reference.dict a dictionnary for the refrence genome