DASVC - De-novo Assembly Structural Variant Caller

A tool for calling SVs from genome-wide contig alignments.

What does the pipeline do?

1. Aligns a genome (query) to a reference genome (target) using LastZ.
2. Chains the query genome against the target genome using UCSC
3. Nets the chains. This resolves overlapping alignments and inversions.
4. netToMaf mafToSam samToBam
5. Sorts the bam by query
6. Annotates the bam file and chains the query.
7. Calls Structural Variants.

Dependancies (for the full pipeline)

The dependancies are only required if you'd like to run the whole pipeline. Otherwise, you can build you own netted SAM file and run the last step.

1. LASTZ. For aligning contigs to a reference genome (lastz-distrib-1.03.73).
2. LAST. Conversion from MAF to SAM (last/744).
3. UCSC. File conversion, chaining and netting.
4. SNAKEMAKE. Running the pipeline.
5. CMAKE. Building Bamtools.
6. BEDTOOLS. Basic range operations (2.21.0)

Installing

0. Install dependancies
1. get and build code :

git clone --recursive https://github.com/zeeev/DASVC.git
cd DASVC
make

2. Export paths to binaries
3. Modify the config file: "pipeline/config.json"
4. Run Snakemake :

locally with 5 jobs :

snakemake -s Snakefile -j 25 -w 50

cluster with 25 jobs :

snakemake  -c "qsub {params.sge_opts}" -s Snakefile -j 25 -w 50

Annotations added to BAM file

1. "QS" Query start
2. "QE" Query end
3. "QL" Query length
4. "TS" Target start
5. "TE" Target end
6. "MB" Number matching bases in block (=|M)
7. "PI" Percent identity
8. "BI" Block ID (equivalent to query name)
9. "TM" Total matching bases in query sequence
10. "AI" Query order 1,2,3....

#Structural variant (SV) format

The SV calls are in bed format:

1. Target seqid
2. Target start
3. target end
4. SV type (internal is contained within an alignment block)
5. SV length (insertions are in query length)
6. Percent identity in alignment block or for flanking alignment blocks
7. Number of bases matching in alignment block or for flanking alignment blocks
8. Query seqid
9. Query start
10. Query end
11. Sequence (for deletions it's the target sequence and insertions are the query sequence)