最近從公共數據庫下載了一堆bam文件和reference 基因組文件，重新分析外顯子流程時，跑出了“Exception in thread "main" picard.PicardException: New reference sequence does not contain a matching contig for NC_007605”這個錯誤。

源代碼是這樣的：

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

搜了一下，gatk官網給出的解決方式，見鏈接：https://gatkforums.broadinstitute.org/gatk/discussion/10071/question-about-picard-reordersam-new-reference-sequence-does-not-contain-a-matching-contig-for

鏈接給出的解釋是：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

如果不加ALLOW_INCOMPLETE_DICT_CONCORDANCE這個參數的話，系統默認為FALSE，即精確匹配，如果想放松匹配要求的話，則可以在命令行添加參數ALLOW_INCOMPLETE_DICT_CONCORDANCE=TRUE，這樣就不會報錯了。

見修改後的命令行：

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

外顯子分析彈錯解決方案：Exception in thread "main" picard.PicardException: New reference sequence does not contain a matching contig for NC_007605