出现“java.lang.AssertionError: SAM dictionaries are not the same”报错

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

  

原文地址:https://www.cnblogs.com/chenwenyan/p/7040852.html