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】
参考:
【1】http://blog.csdn.net/xubo245/article/details/50858334
【2】 http://blog.csdn.net/xubo245/article/details/50879044
【3】: