运行一下程序时出现“java.lang.AssertionError: SAM dictionaries are not the same”报错
java -jar picard.jar SortVcf I=1000G_phase1.indels.hg19.sites.vcf O=1000G_phase1.indels.hg19.sites.sorted.vcf SEQUENCE_DICTIONARY=hg19.dict
说明要先更新hg19.dict，在做上步之前，先运行如下命令：
java -jar picard.jar UpdateVcfSequenceDictionary I=1000G_phase1.indels.hg19.sites.vcf O=1000G_phase1.indels.hg19.sites.dic.vcf SEQUENCE_DICTIONARY=hg19.dict
运行完后，会得到1000G_phase1.indels.hg19.sites.dic.vcf文件
再输入如下命令：
java -Xmx60g -jar picard.jar SortVcf I=1000G_phase1.indels.hg19.sites.dic.vcf O=1000G_phase1.indels.hg19.sites.sorted.vcf SEQUENCE_DICTIONARY=hg19.dict
出现“java.lang.AssertionError: SAM dictionaries are not the same”报错
原文：http://www.cnblogs.com/chenwenyan/p/7040852.html