SVAS

SVAS( Somatic Variant Analysis Suite) Author: Lingxi Chen

Email: [email protected]

Description

ComplexSV provides scripts for complex structure variation analsyis. Currently, it provides two functionalities:

• [linkage_heatmap.py] Generate read shared linkages for given SV event.
• [read_support.py] Generate supporting split reads for given SV event.

The output files can be visuliazed through https://btdraw.com/ SV modules.

Depencency

User can install the required packages via requirements.txt.

python3
pyvcf==0.6.8
pysam==0.15.3
numpy==1.15.4
docopt==0.6.2

Installation

git clone https://github.com/paprikachan/SVAS.git

Then, please add this directory to your PATH.

export PATH=$PWD/SVAS/:$PATH

Linkage Heatmap

General usage

$python3 linkage_heatmap.py -h
Linkage Heatmap.

Usage:
    linkage_heatmap.py call --bam_fn=IN_FILE --sv_fn=IN_FILE [--out_dir=IN_DIR] [--tenx=STR]
    linkage_heatmap.py -h | --help

Options:
    -h --help           Show this screen.
    --version           Show version.
    --bam_fn=IN_FILE    Path of tumor bam file.
    --sv_fn=IN_FILE     Path of tumor sv vcf file.
    --out_dir=OUT_DIR   Path of out directory, [default: ./]
    --tenx=BOOL         Boolean value, True if the protocal is 10x, otherwise False.

User can check the usability with demo case.

cd ComplexSV
python3 linkage_heatmap.py call --bam_fn=demo_data/tumor.bam --sv_fn=demo_data/tumor.sv.vcf --out_dir=demo_data/ --tenx=True

Understanding Output

The demo output file demo_data/10x.txt starts with "sv" section.

#sv
chr11	76139879	+	chr2	63328429	-   VARTYPE=BND:TRX-tt

It stores the breakpoints information of SV event, ordered by:

chrom_5p	bkpos_5p	strand_5p	chrom_3p	bkpos_3p	strand_3p	meta_info
chr11	76139879	+	chr2	63328429	-	VARTYPE=BND:TRX-tt

where chrom_5p, bkpos_5p, strand_5p respectively stands for the chromosome, position, strand of 5' breakpoint, and chrom_3p, bkpos_3p, strand_3p respectively stands for the chromosome, position, strand of 3' breakpoint. meta_info stores the meta information, such as the variation type of the SV.

The second section is "heatmap" section, it starts with the comment:

#heatmap    linkage_type=10x barcode

where linkage_type specifies the type of read linkage used to count, now we support to show "10x barcode" and "Pair End" linkage type.

For a SV event with two breakpoints, expand the breakpoint with 1000bp, we can generate four region pairs and their shared linkage count matrix.

Region pair 1: vertical region is (bkpos_5p-1000bp, bkpos_5p+1000bp) and horizontal region is (bkpos_5p-1000bp, bkpos_5p+1000bp).

v=chr2:63327429-63329429	h=chr2:63327429-63329429	resolution=100	axis=0,0
63.0,34.0,35.0,32.0,21.0,...
34.0,82.0,56.0,37.0,36.0,...
35.0,56.0,104.0,47.0,40.0,...
32.0,37.0,47.0,84.0,40.0,...
21.0,36.0,40.0,40.0,83.0,...
...

Region pair 2: vertical region is (bkpos_5p-1000bp, bkpos_5p+1000bp) and horizontal region is (bkpos_3p-1000bp, bkpos_3p+1000bp).

v=chr2:63327429-63329429	h=chr11:76138879-76140879	resolution=100	axis=1,0
8.0,14.0,7.0,8.0,11.0,...
9.0,17.0,13.0,14.0,13.0,...
14.0,16.0,17.0,22.0,15.0,...
9.0,14.0,11.0,13.0,13.0,...
8.0,13.0,13.0,16.0,13.0,...
...

Region pair 3: vertical region is (bkpos_3p-1000bp, bkpos_3p+1000bp) and horizontal region is (bkpos_5p-1000bp, bkpos_5p+1000bp).

v=chr11:76138879-76140879	h=chr2:63327429-63329429	resolution=100	axis=0,1
8.0,9.0,14.0,9.0,8.0,...
14.0,17.0,16.0,14.0,13.0,...
7.0,13.0,17.0,11.0,13.0,...
8.0,14.0,22.0,13.0,16.0,...
11.0,13.0,15.0,13.0,13.0,...
...

Region pair 4: vertical region is (bkpos_3p-1000bp, bkpos_3p+1000bp) and horizontal region is (bkpos_3p-1000bp, bkpos_3p+1000bp).

v=chr11:76138879-76140879	h=chr11:76138879-76140879	resolution=100	axis=1,1
80.0,52.0,27.0,42.0,33.0,...
52.0,140.0,56.0,61.0,50.0,...
27.0,56.0,124.0,72.0,50.0,...
42.0,61.0,72.0,152.0,57.0,...
33.0,50.0,50.0,57.0,112.0,...
...

Read Support

General usage

$python3 read_support.py -h
Read Support.

Usage:
    read_support.py call --bam_fn=IN_FILE --sv_fn=IN_FILE [--out_dir=OUT_DIR]
    read_support.py -h | --help

Options:
    -h --help           Show this screen.
    --version           Show version.
    --bam_fn=IN_FILE    Path of tumor bam file.
    --sv_fn=IN_FILE     Path of tumor sv vcf file.
    --out_dir=OUT_DIR   Path of out directory, [default: ./]

User can check the usability with demo case.

cd ComplexSV
python3 read_support.py call --bam_fn=demo_data/tumor.bam --sv_fn=demo_data/tumor.sv.vcf --out_dir=demo_data/

Understanding Output

The demo output file demo_data/simu.junc.reads.txt stores supporting split reads for given SV. It starts with "sv" section.

chrom_5p	bkpos_5p	chrom_3p	bkpos_3p	inner_ins	splits_read_num
chr11	100000	chr1	101000	Inner-Ins:TACCGATAT	10

where inner_ins refers to the detected inner insertion, and splits_read_num refers to the number of supporting split read pairs.

Then, it list all supporting split reads, ordered by:

• read_query_name, the read id;

• read_flags, it consists of flag J, P, r, R, d, where

  Flag	Description
  J	The current read is split read
  P	The paired read of current read is split read
  r	The current read is reverse read
  R	The paired read of current read is reverse read
  d	The current read is duplicated

• read_position, the read start position aligned to reconstructed SV haplotype.

   |<-   5'segment   ->| inner_ins |<- 3'  segment  ->|
   |xxxxxxxxxxxxxxxxxxx|iiiiiiiiiii|xxxxxxxxxxxxxxxxxx|
                  :    ^
         negative : <- 0 -> positive
                  :
  split_read:     xxxxxxxxxxxxxxxxxxxxxxxxxxxx
                  ^
  read_position: -5
  

• read_seq, the read sequence;

• read_qual, the read sequence quality.