基于二代萍虽，鑒定睛廊，分型以及可視化，deleetions, tandem duplications, inversions and translocations.
1 Install
git clone --recursive https://github.com/dellytools/delly.git
cd delly/
make all
或者下載最新版本即可使用
wget https://github.com/dellytools/delly/releases/download/v0.8.7/delly_v0.8.7_linux_x86_64bit
Delly同時支持多線程運算杉编，只需在運行命令行前加
export OMP_NUM_THREADS=8, 線程數(shù)≤ 樣本數(shù)
2 二代reads
bam 文件 必須sorted超全，index，duplicated marked 邓馒，ref必須index嘶朱。
call 輸出為bcf，可以用bcftools 轉(zhuǎn)換
BCF--->VCF
bcftools view 1001.bcf > 1001.vcf
# 多線程
export OMP_NUM_THREADS=8
## call
bam= 1001.sorted.rmdup.bam
ref=ref.fa
delly call -g $ref -o 1001.bcf $bam
## merge 每一個樣本
delay merge -o sites.bcf 1001.bcf, 1002.bcf, ... N.bcf
## 再call一次, 可以同線程進(jìn)行
delly call -g $ref -v sites.bcf -o 1001.geno.bcf 1001.sorted.rmdup.bam
delly call -g $ref -v sites.bcf -o 1002.geno.bcf 1002.sorted.rmdup.bam
## bcftools merge
bcftools merge -m id -0 b -o merged.bcf 1001.geno.bcf 1001.geno.bcf ... N.geno.bcf
## 參數(shù)
# -x exclude.region.txt绒净； 取出某區(qū)域
# -t , call 特定的SV见咒，默認(rèn)ALL （DEL, INS, DUP, INV, BND）；
# -v input VCF/BCF file for genotyping
3. 三代reads
delly lr -y ont -g hg19.fa -x hg19.excl input.bam
delly lr -y pb -g hg19.fa -x hg19.excl input.bam
ref
- Tobias Rausch, Thomas Zichner, Andreas Schlattl, Adrian M. Stuetz, Vladimir Benes, Jan O. Korbel.
DELLY: structural variant discovery by integrated paired-end and split-read analysis.
Bioinformatics. 2012 Sep 15;28(18):i333-i339.
https://doi.org/10.1093/bioinformatics/bts378
