PINDEL检测结构变异

PINDEL检测结构变异

输入：
1.配置文件 ：

simulated_sample_1.bam  250     SAMPLE1
simulated_sample_2.bam  250     SAMPLE2
simulated_sample_3.bam  250     SAMPLE3
**注**：bam文件必须samtools index建立索引
pindel -i <bam_config_file> -f <reference.fa> -o <output_prefix> -c <name_of_chromosome\ALL>

例：pindel -i simulated_config.txt -f simulated_reference.fa -o bamtest -c ALL
-c 表示染色体，ALL就是所有染色体（默认）
结果输出根据变异类型不同分成以下几种文件
Variant types reported by Pindel
D = deletion
SI = short insertion
INV = inversion
TD = tandem duplication
LI = large insertion
BP = unassigned breakpoints
The reported larger insertion (LI) record is rather different than other types of variants. Here is the format: index, type(LI), ChrID, chrName, left breakpoint, number of supporting reads for the left coordinate, right breakpoint, number of supporting reads for the right coordinate.
For example:
190 LI ChrID chr1 1000002 5 1000000 6

As there may be sequence similarity around the breakpoint, we may see that the right coordinate may be smaller than the left one.
2.转成vcf格式：

pindel2vcf -r <参考基因组文件> -R <参考基因组名称> -d 参考基因组日期 -p <pindel输出文件> -e <最小的reads数>
pindel2vcf -r simulated_reference.fa -R simulated -d 20100101 -p bamtest_D -e 5