环境：
ubunut
BWA
samtools
wgsim
bwa.kit工具
1.数据下载：需要在bwa.kit下
bwa.kit/run-gen-ref hs38DH
2.串产生：
hadoop@Mcnode1:~/cloud/adam/xubo/data/hs38DH$ wgsim -N 1000 -1 10 hs38DH.fa <span style="font-family: Arial,Helvetica,sans-serif; font-size: 12px;">hs38DHSE1N10000L10F1.fq </span> /dev/null
将文件移到
<pre name="code" class="plain">~/cloud/adam/xubo/data/hs38DH/test20160415
3.匹配+评价
hadoop@Mcnode1:~/cloud/adam/xubo/data/hs38DH/test20160415$ bwa aln ../hs38DH.fa hs38DHSE1N10000L10F1.fq >hs38DHSE1N10000L10F1.sai [bwa_aln] 17bp reads: max_diff = 2 [bwa_aln] 38bp reads: max_diff = 3 [bwa_aln] 64bp reads: max_diff = 4 [bwa_aln] 93bp reads: max_diff = 5 [bwa_aln] 124bp reads: max_diff = 6 [bwa_aln] 157bp reads: max_diff = 7 [bwa_aln] 190bp reads: max_diff = 8 [bwa_aln] 225bp reads: max_diff = 9 [bwa_aln_core] calculate SA coordinate... 0.10 sec [bwa_aln_core] write to the disk... 0.00 sec [bwa_aln_core] 9935 sequences have been processed. [main] Version: 0.7.12-r1039 [main] CMD: bwa aln ../hs38DH.fa hs38DHSE1N10000L10F1.fq [main] Real time: 0.195 sec; CPU: 0.119 sec hadoop@Mcnode1:~/cloud/adam/xubo/data/hs38DH/test20160415$ bwa samse ../hs38DH.fa hs38DHSE1N10000L10F1.sai hs38DHSE1N10000L10F1.fq >hs38DHSE1N10000L10F1.sam [bwa_aln_core] convert to sequence coordinate... 0.04 sec [bwa_aln_core] refine gapped alignments... 0.00 sec [bwa_aln_core] print alignments... 0.02 sec [bwa_aln_core] 9935 sequences have been processed. [main] Version: 0.7.12-r1039 [main] CMD: bwa samse ../hs38DH.fa hs38DHSE1N10000L10F1.sai hs38DHSE1N10000L10F1.fq [main] Real time: 0.154 sec; CPU: 0.086 sec hadoop@Mcnode1:~/cloud/adam/xubo/data/hs38DH/test20160415$ samtools flagstat hs38DHSE1N10000L10F1.sam 9935 + 0 in total (QC-passed reads + QC-failed reads) 0 + 0 secondary 0 + 0 supplementary 0 + 0 duplicates 9907 + 0 mapped (99.72% : N/A) 0 + 0 paired in sequencing 0 + 0 read1 0 + 0 read2 0 + 0 properly paired (N/A : N/A) 0 + 0 with itself and mate mapped 0 + 0 singletons (N/A : N/A) 0 + 0 with mate mapped to a different chr 0 + 0 with mate mapped to a different chr (mapQ>=5) hadoop@Mcnode1:~/cloud/adam/xubo/data/hs38DH/test20160415$ bwa aln ../hs38DH.fa hs38DHSE1N10000L hs38DHSE1N10000L10F1.fq hs38DHSE1N10000L10F1.sai hs38DHSE1N10000L10F1.sam hs38DHSE1N10000L70F1.fq hadoop@Mcnode1:~/cloud/adam/xubo/data/hs38DH/test20160415$ bwa aln ../hs38DH.fa hs38DHSE1N10000L70F1.fq >hs38DHSE1 hs38DHSE1L10000F1.fq hs38DHSE1N10000L10F1.fq hs38DHSE1N10000L10F1.sai hs38DHSE1N10000L10F1.sam hs38DHSE1N10000L70F1.fq hadoop@Mcnode1:~/cloud/adam/xubo/data/hs38DH/test20160415$ bwa aln ../hs38DH.fa hs38DHSE1N10000L70F1.fq >hs38DHSE1N10000L70F1.sai [bwa_aln] 17bp reads: max_diff = 2 [bwa_aln] 38bp reads: max_diff = 3 [bwa_aln] 64bp reads: max_diff = 4 [bwa_aln] 93bp reads: max_diff = 5 [bwa_aln] 124bp reads: max_diff = 6 [bwa_aln] 157bp reads: max_diff = 7 [bwa_aln] 190bp reads: max_diff = 8 [bwa_aln] 225bp reads: max_diff = 9 [bwa_aln_core] calculate SA coordinate... 0.72 sec [bwa_aln_core] write to the disk... 0.00 sec [bwa_aln_core] 9935 sequences have been processed. [main] Version: 0.7.12-r1039 [main] CMD: bwa aln ../hs38DH.fa hs38DHSE1N10000L70F1.fq [main] Real time: 0.779 sec; CPU: 0.734 sec hadoop@Mcnode1:~/cloud/adam/xubo/data/hs38DH/test20160415$ bwa samse ../hs38DH.fa hs38DHSE1N10000L70F1.sai hs38DHSE1N10000L70F1.fq >hs38DHSE1N10000L70F1.sam [bwa_aln_core] convert to sequence coordinate... 0.04 sec [bwa_aln_core] refine gapped alignments... 0.01 sec [bwa_aln_core] print alignments... 0.03 sec [bwa_aln_core] 9935 sequences have been processed. [main] Version: 0.7.12-r1039 [main] CMD: bwa samse ../hs38DH.fa hs38DHSE1N10000L70F1.sai hs38DHSE1N10000L70F1.fq [main] Real time: 0.207 sec; CPU: 0.109 sec hadoop@Mcnode1:~/cloud/adam/xubo/data/hs38DH/test20160415$ samtools flagstat hs38DHSE1N10000L70F1.sam 9935 + 0 in total (QC-passed reads + QC-failed reads) 0 + 0 secondary 0 + 0 supplementary 0 + 0 duplicates 9567 + 0 mapped (96.30% : N/A) 0 + 0 paired in sequencing 0 + 0 read1 0 + 0 read2 0 + 0 properly paired (N/A : N/A) 0 + 0 with itself and mate mapped 0 + 0 singletons (N/A : N/A) 0 + 0 with mate mapped to a different chr 0 + 0 with mate mapped to a different chr (mapQ>=5)
最后得出匹配的准确率在96%左右
