DESCRIPTION
==============
TIDDIT: Is a tool to used to identify  chromosomal rearrangements using Mate Pair or Paired End sequencing data. TIDDIT identifies intra and inter-chromosomal translocations, deletions, tandem-duplications and inversions, using supplementary alignments as well as discordant pairs.

TIDDIT has two analysis modules. The sv mode, which is used to search for structural variants. And the cov mode that analyse the read depth of a bam file and generates a coverage report.


INSTALLATION
==============
TIDDIT requires standard c++/c libraries, python 2.7 or 3.6, cython, and Numpy. To compile TIDDIT, cmake must be installed. 
samtools is reuquired for reading cram files (but not for reading bam).

```
git clone https://github.com/SciLifeLab/TIDDIT.git
```

To install TIDDIT:
```
cd TIDDIT
./INSTALL.sh
```
The install script will compile python and use pip to install the python dependencies
TIDDIT is run via the TIDDIT.py script:
```

python TIDDIT.py --help
python TIDDIT.py  --sv --help
python TIDDIT.py  --cov --help
```

TIDDIT may be installed using bioconda:

	conda install tiddit
	
Next, you may run TIDDIT like this:

	tiddit --help
	tiddit --sv
	tiddit --cov

TIDDIT is also distributed with a Singularity environment (http://singularity.lbl.gov/index.html). Type the following command to download the container:

    singularity pull --name TIDDIT.simg shub://J35P312/TIDDIT:latest

Type the following to run tiddit:

    singularity exec TIDDIT.simg TIDDIT.py

You may also build it yourself (if you have sudo permisions)

    sudo singularity build TIDDIT.simg Singularity

The singularity container will download and install the latest commit on the scilifelab branch of TIDDIT.
The "versioned_singularity" folder contains singularity recipes for installing certain releases of TIDDIT.
These releases may also be downloaded through singularity hub

	singularity pull --name TIDDIT.simg shub://J35P312/TIDDIT:2.7.1

The SV module
=============
The main TIDDIT module, detects structural variant using discordant pairs, split reads and coverage information

    python TIDDIT.py --sv [Options] --bam in.bam


TIDDIT support streaming of the bam file:

   samtools view -buh in.bam |  python TIDDIT.py --sv [Options] --bam /dev/stdin

Optionally, TIDDIT acccepts a reference fasta for GC correction:

    python TIDDIT.py --sv [Options] --bam bam --ref reference.fasta


Reference is required for analysing cram files:

    python TIDDIT.py --sv [Options] --bam in.cram --ref reference.fasta


Where bam is the input bam or cran file. And reference.fasta is the reference fasta used to align the sequencing data: TIDDIT will crash if the reference fasta is different from the one used to align the reads. The reads of the input bam file must be sorted on genome position.

The reference is required for analysing cram files.

NOTE: It is important that you use the TIDDIT.py wrapper for SV detection. The TIDDIT binary in the TIDDIT/bin folder does not perform any clustering, it simply extract SV signatures into a tab file.

TIDDIT may be fine tuned by altering these optional parameters:

    -o - The prefix of the output files(default = output)
        
    -i - The maximum allowed insert size of a normal pair. Pairs having larger insert 
         than this is treated as discordant pairs. Default is 99.9th percentile + 100 bp
                        
    -d - The pair orientation, use this setting to override the automatic orientation selection

    -l - The density parameter, to create a cluster, more than l signals (split reads+ discordant pairs) must be present, signals are added to a cluster if they are neighbouring atleast this  number of signals (defualt 3, minimum 2)
            
    -p - The minimum number of discordant pairs and supplementary alignments used to call large SV. Default is 3
    
    -r - The minimum number of supplementary alignments used to call small SV. Default is 3
            
    -q - The minimum mapping quality of the discordant pairs/supplementary alignments 
         forming a variant. Default value is 5.

    -n - The ploidy of the organism ,(default = 2)

    --force_ploidy - set the ploidy of all chromosomes to -n (including the sex chromosomes), this option will disable the ploidy estimation.
                     This option is meant to be used for low quality data or for species having equal ploidy across all chromosomes

output:

TIDDIT SV module produces three output files, a vcf file containing SV calls, a tab file describing the coverage across the genome in bins of size 50 bp, and a tab file dscribing the estimated ploidy and coverage across each contig.

Useful settings:


In noisy datasets you may get too many small variants. If this is the case, then you may increase the -l parameter, or set the -i parameter to a high value (such as 2000) (on 10X linked read data, I usually set -l to 5).
         
                                
The cov module
==============
Computes the coverge of different regions of the bam file

    python TIDDIT.py --cov [Options] --bam bam
    
optional parameters:

    -o - the prefix of the output files
    -z - compute the coverage within bins of a specified size across the entire genome, default bin size is 500
    -u - do not print per bin quality values
    -w - generate a wig file instead of bed
 --ref - reference sequence (fasta), required for reading cram file.

Filters
=============
TIDDIT uses four different filters to detect low quality calls. The filter field of variants passing these tests are set to "PASS". If a variant fail any of these tests, the filter field is set to the filter failing that variant. These are the four filters empoyed by TIDDIT:

    Expectedlinks
	Less than <p_ratio> fraction of the spanning pairs or <r_ratio> fraction reads support the variant
    FewLinks
        The number of discordant pairs supporting the variant is too low compared to the number of discordant pairs within that genomic region.
    Unexpectedcoverage
        High coverage
    Smear
        The two windows that define the regions next to the breakpoints overlap.

Failed Variants may be removed using tools such as VCFtools or grep. Removing these variants greatly improves the precision of TIDDIT, but may reduce the sensitivity. It is adviced to remove filtered variants or prioritize the variants that have passed the quality checks.
This command may be usedto filter the TIDDIT vcf:

	grep -E "#|PASS" input.vcf > output.filtered.vcf

Quality column
=============
The scores in the quality column are calculated using non parametric sampling: 1000 points/genomic positions are sampled across each chromosome. And the number of read-pairs and reads spanning these points are counted.
The variant support of each call is compared to these values, and the quality column is set to he lowest percentile higher than the (variant support*ploidy).

Note: SVs usually occur in repetetive regions, hence these scores are expected to be relatively low. A true variant may have a low score, and the score itself depends on the input data (mate-pair vs pe for instance).

Contents of the VCF INFO field
=============
The INFO field of the VCF contains the following entries:

    SVTYPE
        Type of structural variant(DEL,DUP,BND,INV,TDUP)
    END
        End position of an intra-chromosomal variant
    LFA
        The number of discordant pairs at the the first breakpoint of the variant
    LFB
	The number of discordant pairs at the the second breakpoint of the variant
    LTE
        The number of discordnat pairs that form the structural variant.
    COVA
        Coverage on window A
    COVM
        The coverage between A and B
    COVB
        Coverage on window B
    CIPOS
        start and stop positon of window A
    CIEND
        start and stop position of window B
    QUALA
        The average mapping quality of the reads in window A
    QUALB
        The average mapping quality of the reads in window B

The content of the INFO field can be used to filter out false positives and to gain more understanding of the structure of the variant. More info is found in the vcf file. 
Merging the vcf files
=====================
I usually merge vcf files using SVDB (https://github.com/J35P312)

svdb --merge --vcf file1.vcf file2.vcf --bnd_distance 500 --overlap 0.6 > merged.vcf

Merging of vcf files could be useful for tumor-normal analysis or for analysing a pedigree. But also to combine the output of multiple callers.

Tumor normal example
===================

run the tumor sample using a lower ratio treshold (to allow for subclonal events, and to account for low purity)

python TIDDIT.py --sv --p_ratio 0.10 --bam tumor.bam -o tumor --ref reference.fasta
grep -E "#|PASS" tumor.vcf > tumor.pass.vcf

run the normal sample

python TIDDIT.py --sv --bam normal.bam -o normal --ref reference.fasta
grep -E "#|PASS" normal.vcf > normal.pass.vcf

merge files:

svdb --merge --vcf tumor.pass.vcf normal.pass.vcf --bnd_distance 500 --overlap 0.6 > Tumor_normal.vcf

The output vcf should be filtered further and annotated (using a local-frequency database for instance)

Annotation
==========
genes may be annotated using vep or snpeff. NIRVANA may be used for annotating CNVs, and SVDB may be used as a frequency database

Algorithm
=========

Discordant pairs and split reads (supplementary alignments) are extracted and stored in the ".signals.tab" file. A discordant pair is any pair having a larger insert size than the  -i paramater, or a pair where the reads map to different chromosomes.
supplementary alignments and discordant pairs are only extracted if their mapping quality exceed the -q parameter.

The most recent version of TIDDIT uses an algorithm similar to DBSCAN: A cluster is formed if -l or more signals are located within the -e distance. Once a cluster is formed, more signals may be added if these signals are within the
-e distance of -l signals within a cluster.

A cluster is rejected if it contains less than -r plus -p signals. If the cluster is rejected, it will not be printed to the vcf file.

If the cluster is not rejected, it will be printed to file, even if it fails any quality filter. 

The sensitivity and precision may be controlled using the -q,r,p, and -l parameters. 

LICENSE
==============
All the tools distributed with this package are distributed under GNU General Public License version 3.0 (GPLv3).