外显子分析弹错解决方案：Exception in thread "main" picard.PicardException: New reference sequence does

Posted 2020-10-12 橙子牛奶糖

最近从公共数据库下载了一堆bam文件和reference 基因组文件，重新分析外显子流程时，跑出了“Exception in thread "main" picard.PicardException: New reference sequence does not contain a matching contig for NC_007605”这个错误。

源代码是这样的：

java -jar picard.jar ReorderSam     I=original.bam     O=reordered.bam     R=reference.fasta     CREATE_INDEX=TRUE

搜了一下，gatk官网给出的解决方式，见链接：https://gatkforums.broadinstitute.org/gatk/discussion/10071/question-about-picard-reordersam-new-reference-sequence-does-not-contain-a-matching-contig-for

链接给出的解释是：By default the tool requires an exact match -- to relax that requirement, use ALLOW_INCOMPLETE_DICT_CONCORDANCE

ALLOW_INCOMPLETE_DICT_CONCORDANCE=Boolean，

If true, then allows only a partial overlap of the BAM contigs with the new reference
sequence contigs. By default, this tool requires a corresponding contig in the new
reference for each read contig Default value: false. This option can be set to ‘null‘ to
clear the default value. Possible values: {true, false}

如果不加ALLOW_INCOMPLETE_DICT_CONCORDANCE这个参数的话，系统默认为FALSE，即精确匹配，如果想放松匹配要求的话，则可以在命令行添加参数ALLOW_INCOMPLETE_DICT_CONCORDANCE=TRUE，这样就不会报错了。

见修改后的命令行：

java -jar picard.jar ReorderSam     I=original.bam     O=reordered.bam     R=reference.fasta     CREATE_INDEX=TRUE
    ALLOW_INCOMPLETE_DICT_CONCORDANCE=true