LUMPY鉴定SV

LUMPY，一款鉴定SV软件，基于read-pair, split-read, read-depth的方法。read-pair即成对儿reads比对位置是否等于插入片段长度，split-read即read可被split；read-depth即duplication。

githup：https://github.com/arq5x/lumpy-sv

其流传如下所示；

简单流程

• 比对 得到bam文件

bwa mem -R "@RG\tID:id\tSM:sample\tLB:lib" human_g1k_v37.fasta sample.1.fq sample.2.fq \
    | samblaster --excludeDups --addMateTags --maxSplitCount 2 --minNonOverlap 20 \
    | samtools view -S -b - \
    > sample.bam

• 调取discordant paired-end 比对（即不是proper mapping）

samtools view -b -F 1294 sample.bam > sample.discordants.unsorted.bam

• 调取split-read 比对; lumpy自带脚本进行调取

samtools view -h sample.bam \
    | scripts/extractSplitReads_BwaMem -i stdin \
    | samtools view -Sb - \
    > sample.splitters.unsorted.bam

• 对bam进行sort

samtools sort sample.discordants.unsorted.bam sample.discordants
samtools sort sample.splitters.unsorted.bam sample.splitters

• 运行lumpy

lumpyexpress \
    -B sample.bam \
    -S sample.splitters.bam \
    -D sample.discordants.bam \
    -o sample.vcf
## 如果有多个样本，则用逗号分隔即可
lumpyexpress \
    -B sample1.bam,sample2.bam,sample3.bam \
    -S sample1.splitters.bam,sample2.splitters.bam,sample3.splitters.bam \
    -D sample1.discordants.bam,sample2.discordants.bam,sample3.discordants.bam \
    -o multi_sample.vcf

• SVTyper 进行genotype分析

svtyper \      
    -B sample.bam \
    -S sample.splitters.bam \
    -i sample.vcf
    > sample.gt.vcf