1， 什么是GATK？

The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute to analyse next-generation resequencing data.

The toolkit offers a wide variety of tools, with a primary focus on variant discovery and genotyping as well as strong emphasis on data quality assurance.

Its robust architecture, powerful processing engine and high-performance computing features make it capable of taking on projects of any size.

2， 如何用GATK call SNP？

用来call snp的数据为经过处理过的bam文件。如何处理另见博文。用到的工具为HaplotypeCaller。假如我有四个bam文件，

LC17-1_L005.sorted.rmp.rg.recal.bam，

LC17-2_L008.sorted.rmp.rg.recal.bam，

RC17-1_L003.sorted.rmp.rg.recal.bam，

RC17-3_L004.sorted.rmp.rg.recal.bam，

都是经过处理，符合GATK要求的bam文件，这四个文件都属于样本C17,我现在要用对样本C17 call snp， 具体命令如下：

 java -jar ./GenomeAnalysisTK.jar -nct 50 -T HaplotypeCaller -R RAP_cDAN.fasta  \

-I LC17-1_L002.sorted.rmp.rg.recal.bam -I LC17-1_L005.sorted.rmp.rg.recal.bam \

-I LC17-2_L006.sorted.rmp.rg.recal.bam -I LC17-2_L008.sorted.rmp.rg.recal.bam \

-I LC17-3_L002.sorted.rmp.rg.recal.bam -I RC17-1_L003.sorted.rmp.rg.recal.bam \

-I RC17-2_L004.sorted.rmp.rg.recal.bam -I RC17-3_L004.sorted.rmp.rg.recal.bam \

-o gatk.vcf

以上几行命令要在同一行，所以看到每行最后有换行符，工具选用的是GATK中的HaplotypeCaller，

-R后跟参考序列，-I 后是bam文件，这几个bam文件都属于一个sample, -o后跟输出文件名字。

-nct 是指定线程数，目前并不能多线程，只能用一个cpu。

结果文件就为gatk.vcf。