SVhawkeye is a tool for verifying structural variation support and drawing quickly from bam files, also, SVhawkeye can draw RNA structure from bam files on isoseq, and SVhawkeye can draw SNP and indel structure and draw depth distribution by your range input.
- Detailed mapping and base information for each read in the interval
- Drawing the Structural Graphics of Reads
- Output genotype
apply to bam files of longreads data, like ONT(Oxford Nanopore Technologies) or PacBio data. Currently, it is not suitable for PE reads from NGS.
- platorm data: ONT(Oxford Nanopore Technologies) or PacBio data, eg.
- sequence data: wgs,wes,isoseq,...
- structure display: structural variation, SNP, INDEL, RNA, cnv-depth
- sv genotyping
Yuhui Xiao, Fan Liang
git clone git@github.com:yywan0913/SVhawkeye.git
cd SVhawkeye
chmod -R 755 haweye.py
./haweye.py --helpDepends：
-
python2 or python3
-
python package: pysam
-
R（any version）
-
R package: getopt, data.table,RColorBrewer
- sample.bam(sample.bam.bai),support Multi-sample，comma-separated,for example: -i A.bam,B.bam,C.bam,...
- bed or vcf file,for example:-b input.bed or -b input.vcf -f vcf
- maybe reference fasta , genePred file. but not must.
DEL:deletion
- SV Judgment:
- show:
INS：insertion
- SV Judgment:
- show:
DUP:duplication
- SV Judgment:
- show:
INV:inversion
- SV Judgment:
- show:
TRA:translocation
- SV Judgment:
- show:
Split mapping were filled with color.
RNA structure
- RNA structure form isoseq:
trio structure
- snp indel ... trio:
cnv structure(depth)
- depth distribution:
./hawkeye.py regiondepth_browse -i HG002_GRCh38.haplotag.10x.bam -o cnvout/ -r chr2:226468627-226471765 -F png
optional arguments:
./hawkeye.py -h
commands:
sv_browse fast draw Structural variation or snp-inDel as IGV.
snpindel_browse fast draw snp or indel variation as IGV
sv_genotyping recall sv of existing input vcf file.
rna_browse display isoform structure from iso-seq
regiondepth_browse display depth distribution of your region
./hawkeye.py sv_browse
Options:
-h, --help show this help message and exit
-i FILE, --bams=FILE set the input bam file. mark=","; [required:True]
-g GENOME, --genome=GENOME
set reference,support:hg19/hg38;while,other genome
also can draw but no annotation; [default:hg19]
-b FILE, --bedvcf=FILE
set the input bed or vcf file; [required=True]
-r FILE, --reffa=FILE
set the reference fasta file of inputbam, when
region<210bp and which can dispaly ref base;
[default:None]
-o Dir, --outdir=Dir set output dirname; [default: ./]
-t <class 'int'>, --thread=<class 'int'>
Number of additional threads to use ; [default:0]
-q num, --quanlty=num
set reads mapping quanlty for filter; [default: 20
(means Q20)]
-I <class 'float'>, --identity=<class 'float'>
set min identity of mapping reads for filter;
[default: 0.6]
-d <class 'int'>, --extend=<class 'int'>
set region extend length; [default:1000bp]
-f vcf/bed, --infmt=vcf/bed
set input format:vcf or bed; [default:bed]
-F png/pdf, --outfmt=png/pdf
set out picture format; [default:png]
-l <class 'int'>, --sv_min_length=<class 'int'>
Minimum length of SV to be reported; [default:50]
if input bed,format:
| #chromosome | start | end | type | chromosome2 | start2 | end2 |
|---|---|---|---|---|---|---|
| 1 | 1288171 | 1290193 | ||||
| 9 | 278819 | 279211 | TRA | 14 | 1427822 | 1429136 |
haweye.py sv_browse -i father.bam,mather.bam,children.bam -g hg19 -b igv.bed -o testdir -t 3
if input vcf,format:
| #CHROM | POS | ID | REF | ALT | QUAL | FILTER | INFO | FORMAT | sample |
|---|---|---|---|---|---|---|---|---|---|
| 5 | 17101355 | sv549 | N | . | pass | SVLEN=107;SVTYPE=DEL;END=17101462 | GT | 0/1 |
SVhaweye.py -i tumor.bam,normal.bam -b test.vcf --format vcf -d 1000 -o test -g hg19
SVhaweye.py -i sample.bam -b test.vcf --format vcf -o test -g hg38 -q 20 -fo pdf
- tree
├── bedpysamout
│---└── HG002_GRCh38.haplotag.10x.bam_chr14_105772449_105860085
├── figure
│---└── chr14_105773449_105859085.e1000.png
├── input.bed
├── new.test.vcf
└── script
│---└── Rigvfrompysam.sh
- HG002_GRCh38.haplotag.10x.bam_chr14_105772449_105860085 :
|Chr|RefStart|RefEnd|QueryStart|QueryEnd|ReadsLen|Mapq|Identity|Strand|Color|Type|Readsorder|ReadsID| |chr14|105761683|105773457|0|11754|11755|60|NA|+|0|normal|13|m64014_181210_152538/159122871/ccs| |chr14|105761697|105772813|1|11103|11102|60|NA|-|0|normal|1|m64018_190129_193747/10749818/ccs| |chr14|105765546|105773455|1407|9307|9306|60|NA|-|1|DEL--chr14_105773455-105859091:85637|10.01|m64020_190123_225958/110167169/ccs| |chr14|105859091|105860456|1|1407|9306|60|NA|-|1|ins--chr14_105859685-105859686:51@@DEL--chr14_105773455-105859091:85637|10|m64020_190123_225958/110167169/ccs| |chr14|105766543|105773455|0|6913|10691|60|NA|+|2|DEL--chr14_105773455-105859091:85637|11|m64014_181210_152538/174458956/ccs|
- new.test.vcf:
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=DA,Number=1,Type=Integer,Description="# number of high-quality reads(depth)">
##FORMAT=<ID=DV,Number=1,Type=Integer,Description="# number of high-quality variant reads">
##FORMAT=<ID=DO,Number=1,Type=Integer,Description="# number of high-quality other variant reads">
|#CHROM|POS|ID|REF|ALT|QUAL|FILTER|INFO|FORMAT|HG002_GRCh38.haplotag.10x|
|chr14|105773449|pbsv.DEL.38747|refseq|T|.|PASS|SVTYPE=DEL;END=105859085;SVLEN=-85636|GT:DV:DA:DO|0/1:10:35:0|
If you have any questions, please contact the following folks:
Yuhui Xiao 651874494@qq.com