Picard报错“MAPQ should be 0 for unmapped read”的解决方法

picard对bwa生成的sam文件进行reorder时，报错如下：

Getting Help Exception in thread "main" htsjdk.samtools. SAM Format Exception: Error parsing text SAM file. MAPQ should be 0 for unmapped read.; File B2.sam; Line 18676 Line: ST-E00126:284:H37TJALXX:8:1101:4158:1872 101

解决办法：在命令行最后再加上 VALIDATION_STRINGENCY=LENIENT

可成功运行

Picard报错“MAPQ should be 0 for unmapped read”的解决方法

原文：http://www.cnblogs.com/zkkaka/p/6211922.html