About the Software
PBHoney is an implementation of two variant-identification approaches designed to exploit the high mappability of long reads (i.e., greater than 10,000 bp). PBHoney considers both intra-read discordance and soft-clipped tails of long reads to identify structural variants.
- samtools 0.1.17
- blasr 126.96.36.199046
- python 2.7
- h5py 2.0.1
- pysam 0.7.4
- numpy 1.6
Note: If you have PacBio's SMRTAnalysis suite v2.1, all of these requirements will be met.
- Edit setup.sh and change $SWEETPATH to the full directory where you've placed the package.
- To automatically place the package into your environment, add > source
/setup.sh to your .bash_profile
- Be sure to source your .bash_profile (or just setup.sh) before using Honey
For more details on each step in the pipeline, see the README below.
Beginning with a mapped bam, you'll use Honey.py to execute the stages 'pie', 'tails', 'spots'.
- Honey.py pie
- Extract the soft-clipped tails and attempt to remap them
- Honey.py tails
- Cluster the tail-mapping information to make genomic breakpoints
- Honey.py spots
- Look for genomic variants within the span of reads.
- REQUIRED : The MD Tag MUST be present in the bam
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