3000份水稻重测序数据全部公开

感觉最近接触的生物信息学知识越多，越对大数据时代的到来更有同感了。现在的研究者，其实很多都可以自己在家里做了，大量的数据基本都是公开的， 但是一个人闭门造车成就真的有限，与他人交流的思想碰撞还是蛮重要的。

https://aws.amazon.com/cn/blogs/aws/new-aws-public-data-set-3000-rice-genome/ https://aws.amazon.com/cn/public-data-sets/3000-rice-genome/ https://wiki.dnanexus.com/Featured-Projects/3000-rice-genomes 

这里面列出了3000多份水稻全基因组测序数据，都共享在亚马逊云上面，是全基因组的双端测序数据，共3,024个水稻数据，比对到了五种不同的水稻参考基因组上面，而且主要是用GATK来找差异基因的。 而且，数据收集者还给出了一个snp calling的标准流程！

其采用的找变异流程如下：

1. SNP Pipeline Commands

3. 1. Index the reference genome using bwa index

5.   /software/bwa-0.7.10/bwa index /reference/japonica/reference.fa

7. 2. Align the paired reads to reference genome using bwa mem.

8.   Note: Specify the number of threads or processes to use using the -t parameter. The possible number of threads depends on the machine where the command will run.

10.   /software/bwa-0.7.10/bwa mem -M -t 8 /reference/japonica/reference.fa /reads/filename_1.fq.gz /reads/filename_2.fq.gz > /output/filename.sam

12. 3. Sort SAM file and output as BAM file

14.   java -Xmx8g -jar /software/picard-tools-1.119/SortSam.jar INPUT=/output/filename.sam OUTPUT=/output/filename.sorted.bam VALIDATION_STRINGENCY=LENIENT CREATE_INDEX=TRUE

16. 4. Fix mate information

18.   java -Xmx8g -jar /software/picard-tools-1.119/FixMateInformation.jar INPUT=/output/filename.sorted.bam OUTPUT=/output/filename.fxmt.bam SO=coordinate VALIDATION_STRINGENCY=LENIENT CREATE_INDEX=TRUE

20. 5. Mark duplicate reads

22.   java -Xmx8g -jar /software/picard-tools-1.119/MarkDuplicates.jar INPUT=/output/filename.fxmt.bam OUTPUT=/output/filename.mkdup.bam METRICS_FILE=/output/filename.metrics VALIDATION_STRINGENCY=LENIENT CREATE_INDEX=TRUE MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=1000

24. 6. Add or replace read groups

26.   java -Xmx8g -jar /software/picard-tools-1.119/AddOrReplaceReadGroups.jar INPUT=/output/filename.mkdup.bam OUTPUT=/output/filename.addrep.bam RGID=readname PL=Illumina SM=readname CN=BGI VALIDATION_STRINGENCY=LENIENT SO=coordinate CREATE_INDEX=TRUE

28. 7. Create index and dictionary for reference genome

30.   /software/samtools-1.0/samtools faidx /reference/japonica/reference.fa

32.   java -Xmx8g -jar /software/picard-tools-1.119/CreateSequenceDictionary.jar REFERENCE=/reference/japonica/reference.fa OUTPUT=/reference/reference.dict

34. 8. Realign Target

36.   java -Xmx8g -jar /software/GenomeAnalysisTK-3.2-2/GenomeAnalysisTK.jar -T RealignerTargetCreator -I /output/filename.addrep.bam -R /reference/japonica/reference.fa -o /output/filename.intervals -fixMisencodedQuals -nt 8

38. 9. Indel Realigner

40.   java -Xmx8g -jar /software/GenomeAnalysisTK-3.2-2/GenomeAnalysisTK.jar -T IndelRealigner -fixMisencodedQuals -I /output/filename.addrep.bam -R /reference/japonica/reference.fa -targetIntervals /output/filename.intervals -o /output/filename.realn.bam

42. 10. Merge individual BAM files if there are multiple read pairs per sample

44.   /software/samtools-1.0/samtools merge /output/filename.merged.bam /output/*.realn.bam

46. 11. Call SNPs using Unified Genotyper

48.   java -Xmx8g -jar /software/GenomeAnalysisTK-3.2-2/GenomeAnalysisTK.jar -T UnifiedGenotyper -R /reference/japonica/reference.fa -I /output/filename.merged.bam -o filename.merged.vcf -glm BOTH -mbq 20 --genotyping_mode DISCOVERY -out_mode EMIT_ALL_SITES