基因数据处理14之BWA三种方式bwa、BWA_SW、BWA_MEM使用

1.构建索引：

bwa index ref.fa

或者从ftp下载，请参考【1】

2.BWA：

bwa.sh为脚本文件

hadoop@Master:~/cloud/adam/xubo/data/test20160310/bwa3sh$ cat bwa.sh 
#!/bin/bash
bwa aln ../GCA_000001405.15_GRCh38/GCA_000001405.15_GRCh38_full_analysis_set.fna ../SRR003161h20.fastq > SRR003161h20t1.sai
bwa samse ../GCA_000001405.15_GRCh38/GCA_000001405.15_GRCh38_full_analysis_set.fna SRR003161h20t1.sai ../SRR003161h20.fastq >SRR003161h20t1.sam

文件的获取请参考【1】和【2】

3.BWA_SW:

bwasw.sh也是脚本文件

hadoop@Master:~/cloud/adam/xubo/data/test20160310/bwasw$ cat bwasw.sh 
#!/bin/bash
bwa bwasw ../GCA_000001405.15_GRCh38/GCA_000001405.15_GRCh38_full_analysis_set.fna ../SRR003161h20.fastq >SRR003161h20t1.sam

4.BWA_MEM:

bwa mem GCA_000001405.15_GRCh38/GCA_000001405.15_GRCh38_full_analysis_set.fna SRR003161h20.fastq >SRR003161h20.sam

具体的格式请参考【3】