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STIX (Structural Variant Index) supports searching every discordant paired-end and split-read alignment from thousands of sample BAMs or CRAMs for the existence of an arbitrary SV. STIX reports a per-sample count of all concurring evidence. From these counts we can, for example, conclude that an SV with high-level evidence in many samples is common and an SV with no evidence is rare.

Usage

usage:   stix <options>
         options:
             -i  index directory
             -s  slop
             -P  padding base piars for query insertion(default 50)
             -p  PED file
             -B  Sharding file
             -Q  Batch queries in table format(left \t right \t len \t SVtype \t ID)
             -T  Threshold to define STIX_ONE(How many supporting reads define a hit) (default:1)
             -c  Alt file column (default 1)
             -d  PED database file
             -r  right SV region
             -l  left SV region
             -f  VCF file
             -a  List of columns to aggregate over
             -F  Filter samples by PED field query
             -j  JSON output
             -t  SV type (DEL,INS,INV,DUP,BND)
             -L  Length of Insertion(use it when -t INS)
             -R  Relative Erorr Threshold to compare the length of query INS and targeted INS (0.0-1.0) (default:0.15)
             -v  Add sample depth to VCF file
             -S  Give only summary
             -D  Give sample depth array
             -V  Verbose mode(print debug information, will increase output file size greatly)

Example

The following example is based on four sample BAMs from the 1000 Genomes project:

samtools view -b s3://1000genomes/phase3/data/NA12812/alignment/NA12812.mapped.ILLUMINA.bwa.CEU.low_coverage.20130415.bam 13 14 > NA12812.13.14.bam
samtools view -b s3://1000genomes/phase3/data/HG00672/alignment/HG00672.mapped.ILLUMINA.bwa.CHS.low_coverage.20120522.bam 13 14 > HG00672.13.14.bam
samtools view -b s3://1000genomes/phase3/data/NA12878/alignment/NA12878.mapped.ILLUMINA.bwa.CEU.low_coverage.20121211.bam 13 14 > NA12878.13.14.bam
samtools view -b s3://1000genomes/phase3/data/HG00674/alignment/HG00674.mapped.ILLUMINA.bwa.CHS.low_coverage.20121211.bam 13 14 > HG00674.13.14.bam

To create an STIX index, use excord to extract discordant paired-end reads and split reads.

mkdir four_alt
wget -O excord https://github.com/brentp/excord/releases/download/v0.2.2/excord_linux64
chmod +x excord
wget ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz

for sample in NA12812.13.14 HG00672.13.14 NA12878.13.14 HG00674.13.14; do
    samtools view -b $sample.bam \
    | ./excord \
        --discordantdistance 500 \
        --fasta hs37d5.fa.gz \
        /dev/stdin \
    | LC_ALL=C sort --buffer-size 2G -k1,1 -k2,2n -k3,3n \
    | bgzip -c > four_alt/$sample.bed.gz
done

Now index with GIGGLE.

giggle index -i "four_alt/*gz" -o four_alt_b -s -f

STIX requires a PED file that needs at least sample name and discordant alignment file name, but can support an arbitrary number of columns. For example:

Sample	Sex	Populationzv    Super_Population	Alt_File
NA12812	1	CEU	EUR	NA12812.13.14.bed.gz
HG00672 2	CHS	EAS	HG00672.13.14.bed.gz
NA12878 2	CEU	EUR	NA12878.13.14.bed.gz
HG00674 1	CHS	EAS	HG00674.13.14.bed.gz

From a PED file create a database/.

stix -i four_alt_b -p test/data/four.ped -d four.ped.db -c 5

STIX can query either a single SV or annotate a VCF file. All queries require a slop parameter that accounts for the variability in the normal fragment size. In most cases use the mean fragments size plus 3 times the fragment size standard deviation.

For individual queries, STIX takes the SV type and the left and right positions of the SV, where left is (by convention) the lower chromosomal position. Since many SVs do not have base pair resolution, STIX takes a genomic range for each side.

stix -i four_alt_db -d four.ped.db -s 500 -t DEL -l 14:68603030-68603035 -r 14:68603738-68603743

Total   0:1 0:0 7:8:11  0:2:1:1
Giggle_File_Id  Sample  Sex Population  Super_Population    Alt_File    Pairend Split
0   HG00672 2   CHS EAS HG00672.13.14.bed.gz    8   0
1   HG00674 1   CHS EAS HG00674.13.14.bed.gz    7   0
2   NA12812 1   CEU EUR NA12812.13.14.bed.gz    7   0
3   NA12878 2   CEU EUR NA12878.13.14.bed.gz    11  0

For a VCF, STIX uses the INFO/SVTYPE field for the SV type and the POS, INFO/END, INFO/CIPOS, and INFO/CIEND fields for the quarry positions. STIX annotates each variant with four fields:

STIX_ZERO gives the number of samples that have no evidence for the SV
STIX_ONE gives the number of samples that have one alignments supporting the SV
STIX_QUANTS has three values that are the quantiles for the per sample count of alignments supporting the SV
STIX_QUANT_DEPTHS has four values that give the number of samples with SV an evidence count that is
1. between 2 and the quantile one value number of alignments
2. between quantile one to quantile two
3. quantile two to quantile three
4. more than quantile three

stix -i four_alt_db -d four.ped.db -s 500 -f 1kg.four.13.14.vcf.gz

Build

git clone https://github.com/ryanlayer/giggle.git
cd giggle
make
cd ..
wget http://www.sqlite.org/2017/sqlite-amalgamation-3170000.zip
unzip sqlite-amalgamation-3170000.zip
git clone https://github.com/ryanlayer/stix.git
cd stix
make

Sample results

DEL

19:12694867-12698924

STIX

STIX_ZERO STIX_ONE STIX_QUANTS STIX_QUANT_DEPTHS
0         0        0,4,11      0,0,1,1

1KG low-coverge SV callset (Sudmant et al., Nature 2015) (VCF, Paper)

#CHROM POS       REF ALT   INFO                                        NA12878 NA12890 NA12889
19     12694867  G   <CN0> CIEND=0,1;CIPOS=0,1;END=12698924            1|1     1|1     1|1

SVTYPER high-coverage genotypes

         GT  GQ  SQ     GL         DP RO AO QR QA RS AS ASC RP AP AB
NA12878  1/1 13  796.49 -82,-3,-2  40 9  30 9  30 0  0  0   9  30 0.77    
NA12890  1/1 10  609.94 -63,-3,-2  31 7  23 7  23 0  0  0   7  23 0.77
NA12889  0/1 139 794.47 -80,-1,-15 68 33 34 32 33 20 0  0   12 33 0.51

LUMPY/SVTYPER high-coverage calls

#CHROM POS       REF ALT   INFO                                        NA12878 NA12890 NA12889
19     12694907  N  <DEL>  CIPOS=-10,69;CIEND=-59,4;END=12698928       1/1     1/1     1/1

High coverage	Low coverage

5:1022803-1025877

STIX

STIX_ZERO STIX_ONE STIX_QUANTS STIX_QUANT_DEPTHS
3         0        0,0,0       0,0,0,0

1KG low-coverge SV callset (Sudmant et al., Nature 2015) (VCF, Paper)

#CHROM POS       REF ALT   INFO                                        NA12878 NA12890 NA12889
5      1022803   C   <CN0> CIEND=-500,1000;CIPOS=-1000,500;END=1025877 1|1     1|1     1|1

SVTYPER high-coverage genotypes

         GT  GQ  SQ   GL          DP  RO  AO QR  QA RS AS ASC RP AP AB
NA12878  0/0 200 0.00 -0,-18,-61  62  62  0  61  0  27 0  0   34 0  0
NA12890  0/0 200 0.00 -0,-23,-78  78  78  0  78  0  37 0  0   41 0  0
NA12889  0/0 200 0.00 -0,-33,-109 110 109 0  109 0  55 0  0   54 0  0

LUMPY/SVTYPER high-coverage calls

N/A

High coverage	Low coverage

4:113985874-113986369

STIX

STIX_ZERO STIX_ONE STIX_QUANTS STIX_QUANT_DEPTHS
0         0        4,8,10      0,1,1,1

1KG low-coverge SV callset (Sudmant et al., Nature 2015) (VCF, Paper)

#CHROM POS        REF ALT   INFO                                        NA12878 NA12890 NA12889
4      113985874  .   <DEL> END=113986369                               0|0     0|0     0|0

SVTYPER high-coverage genotypes

         GT  GQ  SQ      GL         DP RO AO QR QA RS AS ASC RP AP AB
NA12878  1/1 24  1484.47 -152,-6,-3 74 17 56 17 56 0  0  0   17 56 0.77
NA12890  0/1 105 446.67  -46,-1,-11 42 22 19 22 19 0  0  0   22 19 0.46
NA12889  0/1 21  1259.40 -129,-3,-6 71 21 49 21 49 0  0  0   21 49 0.7

LUMPY/SVTYPER high-coverage calls

#CHROM POS        REF ALT   INFO                                        NA12878 NA12890 NA12889
4      113985951  .   <DEL> CIPOS=-12,2;CIEND=-51,12;END=113986325      1/1     0/1     1/1

High coverage	Low coverage

DUP

INS

INV

12:12544868-12546613

STIX

1KG low-coverge SV callset (Sudmant et al., Nature 2015) (VCF, Paper)

#CHROM POS        INFO                                                       NA12878 NA12890 NA12889
12      12544792  END=12546607;CIEND=-21,21;CIPOS=-21,21;AC=4129;AF=0.824481 1|1     1|1     1|1

SVTYPER high-coverage genotypes

         GT  SU PE SR GQ  SQ      GL          DP RO AO QR QA RS AS ASC RP AP AB
NA12878  0/1 58 58 0  114 1478.17 -150,-2,-14 99 39 60 38 59 20 0  2   18 57 0.61
NA12890  1/1 54 54 0  25  1356.74 -139,-5,-3  67 15 51 15 51 0  0  0   15 51 0.77
NA12889  0/1 46 46 0  200 1073.26 -108,-1,-22 94 47 46 47 45 26 0  1   21 44 0.49

LUMPY/SVTYPER high-coverage calls

#CHROM POS        INFO                                   NA12878 NA12890 NA12889
12     12544868   END=12546613;CIPOS=-2,17;CIEND=-15,19; 0/1     1/1     0/1

High coverage	Low coverage

12:47290448-47309758

STIX

1KG low-coverge SV callset (Sudmant et al., Nature 2015) (VCF, Paper)

#CHROM POS      INFO                                                        NA12878 NA12890 NA12889
12     47290470 END=47309756;CIEND=-55,55;CIPOS=-55,55;AC=248;AF=0.0495208  0|0     0|0     1|0

SVTYPER high-coverage genotypes

         GT  SU PE SR GQ  SQ     GL          DP  RO  AO QR  QA RS AS ASC RP AP AB
NA12878  0/0 0  0  0  200 0.00   -0,-39,-130 131 131 0  130 0  64 0  0   66 0  0
NA12890  0/0 0  0  0  200 0.00   -0,-35,-115 116 116 0  115 0  56 0  0   59 0  0
NA12889  0/1 79 56 23 146 578.17 -65,-7,-59  120 87  32 86  31 38 0  9   48 22 0.26

LUMPY/SVTYPER high-coverage calls

#CHROM POS      INFO                                   NA12878 NA12890 NA12889
12     47290448 END=47309758;CIPOS=-3,2;CIEND=-10,5;   0/0     0/0     0/1

High coverage	Low coverage

2:89161083-89185670

STIX

1KG low-coverge SV callset (Sudmant et al., Nature 2015) (VCF, Paper)

N/A

SVTYPER high-coverage genotypes

         GT  SU PE SR GQ  SQ     GL         DP  RO AO QR QA RS AS ASC RP AP AB 
NA12878  0/1 0  0  0  4   53.14  -6,-0,-1   4   1  2  1  2  1  0  2   0  0  0.67
NA12890  0/0 0  0  0  200 0      -0,-28,-93 94  94 0  93 0  42 0  0   51 0  0
NA12889  0/1 68 44 24 143 383.23 -48,-9,-65 115 89 25 88 24 42 0  2   46 22 0.21

LUMPY/SVTYPER high-coverage calls

#CHROM POS      INFO                                   NA12878 NA12890 NA12889
2      89161083 END=89185670;CIPOS=0,0;CIEND=-9,0      0/1     0/0     0/1

High coverage	Low coverage

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Usage

Example

Build

Sample results

DEL

19:12694867-12698924

STIX

1KG low-coverge SV callset (Sudmant et al., Nature 2015) (VCF, Paper)

SVTYPER high-coverage genotypes

LUMPY/SVTYPER high-coverage calls

5:1022803-1025877

STIX

1KG low-coverge SV callset (Sudmant et al., Nature 2015) (VCF, Paper)

SVTYPER high-coverage genotypes

LUMPY/SVTYPER high-coverage calls

4:113985874-113986369

STIX

1KG low-coverge SV callset (Sudmant et al., Nature 2015) (VCF, Paper)

SVTYPER high-coverage genotypes

LUMPY/SVTYPER high-coverage calls

DUP

INS

INV

12:12544868-12546613

STIX

1KG low-coverge SV callset (Sudmant et al., Nature 2015) (VCF, Paper)

SVTYPER high-coverage genotypes

LUMPY/SVTYPER high-coverage calls

12:47290448-47309758

STIX

1KG low-coverge SV callset (Sudmant et al., Nature 2015) (VCF, Paper)

SVTYPER high-coverage genotypes

LUMPY/SVTYPER high-coverage calls

2:89161083-89185670

STIX

1KG low-coverge SV callset (Sudmant et al., Nature 2015) (VCF, Paper)

SVTYPER high-coverage genotypes

LUMPY/SVTYPER high-coverage calls

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