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Users' Guide

LinkedSV is a novel structural variant caller for 10X Genomics (linked-read) sequencing data. It detects deletions, duplications, inversions and translocations using evidence from the barcoded reads.

Table of Contents

Installation

Prerequisites

Most of the source code was written in Python, but the time-consuming steps were written in C++11. It uses htslib to process bam files.

The following software tools and packages are required for the installation of LinkedSV.

  1. c++ compiler (A c++ compiler that supports C++11 is needed to build LinkedSV. Development of the code is performed using g++ v4.8.5)

  2. Python (version: >= 2.7 python 3 is supported)

  3. Python packages: sklearn, scipy, numpy, gzip, psutil, subprocess, bisect, math, argparse, pandas, seaborn, datetime. Among these, math, subprocess, gzip and bisect are included in the python standard library, meaning that they should be already installed with python.

You can use pip to install a python package. You can use the following command to install all the required python packages.

pip install --user sklearn scipy numpy psutil argparse pandas seaborn datetime

The --user tells pip to install the seaborn in your own directory, so that you don't need root access.

If you don't have pip in your system, you can install pip according to the instructions here

  1. SAMtools (version >= 1.5)

  2. BEDTools

  3. perl. A recent version should work. If you have issues with perl, please submit an issue in the issue page.

Compilation

If the above tools and packages are available, you can use the following command to download and compile LinkedSV:

git clone https://github.com/WGLab/LinkedSV.git 
cd LinkedSV/
sh build.sh 

Usage

usage: linkedsv.py [-h] -i input.phased_possorted_bam.bam -d output_directory
                   -r ref.fa [-v version] [--gap_region_bed BED]
                   [--black_region_bed BED] [-t num_thread]
                   [--min_fragment_length INT] [--min_reads_in_fragment INT]
                   [--min_supp_barcodes INT] [--samtools path/to/samtools]
                   [--bedtools path/to/bedtools] [--wgs] [--targeted]
                   [--germline_mode] [--somatic_mode] [--target_region BED]
                   [--gap_distance_cut_off INT] [--save_temp_files]

General usage

The input.phased_possorted_bam.bam is the input bam file, which contains the barcoded reads. LinkedSV read the barcodes from the BX tag in the bam TAG field. We recommend using the phased_possorted_bam.bam file generated by the official Longranger pipeline.

The ref.fasta file is the FASTA file of the reference genome. It should be the same fasta file that was used for alignment. The ref.fasta file should be indexed by samtools. You can use the following command to index a ref.fasta file:

samtools faidx ref.fasta

This command will generate a ref.fasta.fai file in the same directory of the ref.fasta file.

output_directory is the directory where the output files will be generated.

black_region_bed is the blacklist file for filtering SV calls. The blacklist contains a small set of regions that give consistently spurious signal across samples. We prepared black_region_bed for human reference genomes (versions: hg19, b37, hg38), so you don't need to provide it if you use hg19, b37, or hg38.

gap_region_bed is the bed file of gap regions in the reference genome. It is used to filter the SV calls. LinkedSV provides gap_region_bed for human reference genomes (versions: hg19, b37, hg38), so you don't need to provide it if you use hg19, b37, or hg38.

ref_version is used to tell LinkedSV which black_region_bed file and gap_region_bed file should be used. Currently we have generated blacklists for hg19 (style: "chr1"), b37 (style: "1") and hg38 (style: "chr1"). It is highly recommended to spcifiy ref_version if you are using these three versions. The valid values are: hg19, b37, hg38.

If you are using a different reference file, please generate the black_region_bed file and the gap_region_bed file by yourself and specify the --gap_region_bed and --black_region_bed parameters.

If you don't have samtools and bedtools in your path, please specify the path using --samtools and --bedtools.

Use cases:

Detection of germline SVs from whole-genome sequencing

python linkedsv.py -i input.phased_possorted_bam.bam -d path/to/output_dir/ -r hg38.fa -v hg38 -t 4 --germline_mode

The -v hg38 parameter specify that the reference genome is hg38. If you use another version, please change accordingly. We recommend using at least 4 threads to speed up the run. Each thread need 4GB memory.

Detection of germline SVs from targeted sequencing (e.g. whole-exome sequencing)

python linkedsv.py -i phased_possorted_bam.bam -d path/to/output_dir/ -r ref.fasta -v hg38 -t 4 --targeted --target_region path/to/target_region.bed --germline_mode

target_region.bed is a bed file that contains the target regions (capture regions).

Detection of somatic SVs from whole-genome sequencing

python linkedsv.py -i input.phased_possorted_bam.bam -d path/to/output_dir/ -r ref.fasta -v hg38 -t 4 --somatic_mode

Output Files

LinkedSV will output the SV calls, as well as the figures that allow you to visualize the large SV calls.

SV call file

LinkedSV will output three SV call files, prefix.small_deletions.bedpe, prefix.large_cnv.bedpe and prefix.filtered_large_svcalls.bedpe. The prefix.small_deletions.bedpe file contains small deletions detected from short-read information (discordant paired-end reads and local assembly). The prefix.large_cnv.bedpe file contains copy number variants detected from an algorithm based on read depth. The prefix.filtered_large_svcalls.bedpe file contains the filtered SV calls detected from linked-reads using barcode information.

The BEDPE format was defined by BEDtools (https://bedtools.readthedocs.io/en/latest/content/general-usage.html). It can be used to concisely describe disjoint genome features, such as structural variations. We did not use BED format because BED format does not allow inter-chromosomal feature definitions.

The SV call file contains one SV per line with the following tab-delimited columns:

Column Description
chrom1 chrom of breakpoint 1
start1 start position of breakpoint 1
stop1 end position of breakpoint 1
chrom2 chrom of breakpoint 2
start2 start position of breakpoint 2
stop2 end position of breakpoint 2
sv_type SV type inferred from breakpoints
sv_id unique ID of the SV
sv_length SV length
qual quality score
filter filter. 'PASS' if the call passed all filtering steps.
info detailed information of the SV call

For the meaning of "endpoint1_type" and "endpoint2_type", please refer to our manuscript (Citation)

Intermediate files

LinkedSV also outputs an intermediate files:

prefix.bcd21.gz

This file contains the data that can be used to visualize the SV evidence.

LinkedSV will also generate an images directory in the output directory. The figures showing the evidence of the SV are under this directory. Currently, only the evidence of SVs detected from linked-reads using barcode information (in the prefix.filtered_large_svcalls.bedpe file) are plotted.

Visualization of SV calls

After SV calling, LinkedSV will plot high-resolution figures showing the evidence of the SV, so that you can see them intuitively.

Currently, LinkedSV will plot 3 types of evidence:

  1. read depth (for all SV calls)
  2. evidence of decrease of overlapping barcodes between adjcent twin windows (for balanced SV calls)
  3. Heat maps of overlapping barcodes (for all SV calls)

These figures are generated in the images directory under the output directory. The structure of the images directory is:

linkedsv_out_dir
|-- images
    |-- read_depth
        |-- prefix.ID01.read_depth.png
        |-- prefix.ID02.read_depth.png
        
    |-- twin_window_barcode_similarity
        |-- prefix.ID01.breakpoint1.twin_window_barcode_similarity.png
        |-- prefix.ID01.breakpoint2.twin_window_barcode_similarity.png
        |-- prefix.ID02.both_breakpoints.twin_window_barcode_similarity.png 
        
    |-- 2D_heatmap
        |-- prefix.ID01.heatmap.png
        |-- prefix.ID01.heatmap.png

Read depth

Here are some example figures for different SV types. The figures were plotted from the SV calls on the HX1 genome. The dotted blue line showed the average depth across the whole genome. The predicted breakpoints were indicated by vertical red lines. The black line showed the depth of confidently mapped reads (map quality >= 20) and the grey line showed the depth of all reads (map quality >= 0). The black line is in front of the grey line. So if you do not see the grey lines, then the black and grey lines are in the same place (i.e. the region is of high map quality).

Deletion DEL The region between the two red lines has lower read depth.

Duplication DUP The region between the two red lines has higher read depth.

Inversion INV The region between the two red lines has same read depth as the flanking regions.

Twin-window evidence

LinkedSV plots the twin-window evidence for balanced SV events, such as inversions and balanced translocations. The barcodes between two nearby genome locations is highly similar because the two locations are spanned by almost the same set of input HMW DNA molecules. However, due to the genome rearrangement, the reads mapped to the left side and right side of a breakpoint may originate from different locations of the alternative genome and thus have different barcodes.

Dropped barcode similarity between two nearby loci therefore indicates a SV breakpoint. LinkedSV detects this type of evidence by a twin-window method, which uses two adjacent sliding windows to scan the genome and find regions where the barcode similarity between the two nearby window regions are significantly decreased. (Please refer to our manuscript for the detailed explaination: Citation )

Here is an example figure of the twin-window evidence. It was plotted from an inversion call on the HX1 genome. X-axis is the position of the middle of the twin windows. Y-axis is the -log10(P-value), where P-value means the probabity that the overlapping barcodes between the twin windows is less than or equal to the observed number assuming no SV.

In the following figure, the red line showed the predicted breakpoint. Since the P-value is very small at the breakpoints, Y values (-log10(P-value)) are very high and form two peaks at the breakpoints.

Inversion INV

Heat map of overlapping barcodes

LinkedSV also plots the 2D heat maps of overlapping barcodes. This figure is similar to the figure showed by Loupe, which was developped by 10X Genomics. The slight difference is that the color map of LinkedSV is of wider range (0-100).

The resolution is 1000 bp. The color of each dot indicates the number of overlapping barcodes between two genomics positions (X and Y coordinates of the dot).

Some example figures are here.

Deletion DEL

Duplication DUP DUP

Inversion INV

Future extensions

Recently, BGI and Complete Genomics developped single tube long fragment read (stLFR) (Genome Res. 2019), a technology that enables sequence data from long DNA molecules using second-generation sequencing technology. It is based on adding the same barcode sequence to sub-fragments of the original long DNA molecule (DNA co-barcoding). Since this technology is also a barcoded sequencing of long fragments, LinkedSV is planned to support stLFR in the near future.

Citation

If you use LinkedSV in your work, please cite:

Li Fang, Charlly Kao, Michael V Gonzalez, Fernanda A Mafra, Renata Pellegrino da Silva, Mingyao Li, Soren Wenzel, Katharina Wimmer, Hakon Hakonarson, Kai Wang. LinkedSV: Detection of mosaic structural variants from linked-read exome and genome sequencing data. Nature Communications, 10:5585, 2019

Getting Help

Please use the GitHub's Issues page if you have questions.

License Agreement

LinkedSV is under the MIT license.

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