Name: TIDDIT
Owner: Science For Life Laboratory
Description: TIDDIT - structural variant calling
Created: 2015-06-26 11:13:53.0
Updated: 2017-11-08 18:27:11.0
Pushed: 2017-12-13 16:43:16.0
Size: 1930
Language: C++
GitHub Committers
| User | Most Recent Commit | # Commits |
|---|
Other Committers
| User | Most Recent Commit | # Commits |
|---|
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 modes of analysing bam files. 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.
TIDDIT requires standard c++/c libraries, python 2.7, Numpy and scipy. To compile TIDDIT, cmake must be installed.
clone https://github.com/SciLifeLab/TIDDIT.git
To install TIDDIT:
IDDIT
STALL.sh
TIDDIT is run via the TIDDIT.py script:
on TIDDIT.py --help
on TIDDIT.py --sv --help
on TIDDIT.py --cov --help
TIDDIT is also distributed with an experimental Singularity environment (http://singularity.lbl.gov/index.html). This environment could be used to solve issues with the c++ libraries. This environment has been tested with Singularity 2.4.1-dist. You may either use the singularity image (TIDDIT.simg), or install it from the Singularity file.
Type the following to enter a session using the TIDDIT.simg container:
singularity shell TIDDIT.simg
Now you can install and run TIDDIT. type exit to leave the environment:
exit
If you want, you can build the container yourself, then you type the following command:
singularity build TIDDIT_env.simg Singularity
you may need sudo permissions
sudo singularity build TIDDIT_env.simg Singularity
and enter it like this:
singularity shell TIDDIT_env.simg
The main TIDDIT module, detects structural variant using discordant pairs, split reads and coverage information
python TIDDIT.py --sv [Options] --bam bam --ref reference.fasta
Where bam is the input bam 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. 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 3*std+mean insert size
-d - The pair orientation, use this setting to override the automatic orientation selection
-p - The minimum number of discordant pairs and supplementary alignments used to call large SV. Default is 5
-r - The minimum number of supplementary alignments used to call small SV. Default is 5
-q - The minimum mapping quality of the discordant pairs/supplementary alignments
forming a variant. Default value is 10.
-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 100 bp, and a tab file dscribing the estimated ploidy and coverage across each contig.
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
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
The number of discordant pairs/supplementary alignments supporting
the variant is less than 40% of the expected number of supporting reads
FewLinks
The number of discordant pairs supporting the variant is less than 20% of the
discordant pairs within that genomic region.
Unexpectedcoverage
The coverage across the variant is more than 10* the mean 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 failed variants or prioritize the variants that have passed the quality checks.
TIDDIT returns the detected variants into two vcf files, one vcf for intrachromosomal variants, and one for interchromosomal variants. 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
OA
Orientation of the reads in window A
OB
Orientation of the mates in window B
CIPOS
start and stop positon of window A
CIEND
start and stop position of window B
EL
Expected links to window B
ER
Expected number of split reads
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
TIDDIT detects structural variants using supplementary alignments as well as discordant pairs. A discordant pair is defined as any pair of reads having a larger distance than the –insert parameter(which is set to 3*std+average library distance as default). Supplementary aligments are produced by reads where one part of the read aligns to a certain part of the reference, while another part of the same read aligns to a distant region.
TIDDIT performs a linear search for SV signatures within the input Bam file. These signatures are prited to the signals file. Upon searching the entire bam file, TIDDIT starts to cluster these signals using an algorithm similar to DBSCAN. Any set of discordant pairs or supplementary alignments larger or equal to the -p parameter will be analysed and later returned as a structural variant by printing it to the vcf file. TIDDIT will only consider reads that fullfill the -q parameter: reads having lower mapping quality will not be added to a set, and thus will not contribute to the detection of SV.
TIDDIT detects a wide spectra of structural variants, and is able to classify deletions, duplications, inversions and translocations(intrachromosomal and interchromosomal). Variants are classified based on the pair orientation of the reads defining a structural variant, as well as the coverage across the structural variant and the regions where the read pairs are aligned. If TIDDIT is unnable to classify a variant, it will be returned as a break end event.
All the tools distributed with this package are distributed under GNU General Public License version 3.0 (GPLv3).