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3000多份水稻全基因组测序数据

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发表于 2017-2-6 15:24:41 | 显示全部楼层 |阅读模式
转载自我的博客:  http://www.bio-info-trainee.com/1053.html
Posted on 2015年10月16日 3000多份水稻全基因组测序数据共享-主要是突变数据
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/ ... t-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

[Shell] 纯文本查看 复制代码
1. Index the reference genome using bwa index

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

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

   /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

3. Sort SAM file and output as BAM file

   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

4. Fix mate information

   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

5. Mark duplicate reads

   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

6. Add or replace read groups

   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

7. Create index and dictionary for reference genome

   /software/samtools-1.0/samtools faidx /reference/japonica/reference.fa
   
   java -Xmx8g -jar /software/picard-tools-1.119/CreateSequenceDictionary.jar REFERENCE=/reference/japonica/reference.fa OUTPUT=/reference/reference.dict

8. Realign Target 

   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

9. Indel Realigner

   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 

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

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

11. Call SNPs using Unified Genotyper

   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




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