LUMPY鉴定SV

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...

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 "@RGtID:idtSM:sampletLB: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
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