BGISEQ500测序数据，使用picard对多个lane的bam进行dedup时报如下错误：

Exception in thread "main" htsjdk.samtools.util.RuntimeIOException: Read error; BinaryCodec in readmode; file: /path/lane.dedup.realn.recal.bam

参考bcbio/bcbio-nextgen#1392 (comment)
判断应该是bam文件提前中断导致报错，不过从log中看bam的生成没有问题，只有一个Warning

WARNING 2017-06-07 13:57:57 AbstractDuplicateFindingAlgorithm Default READ_NAME_REGEX '[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*' did not match read name 'CL100009742L1C007R055_331190'. You may need to speci
fy a READ_NAME_REGEX in order to correctly identify optical duplicates. Note that this message will not be emitted again even if other read names do not match the regex.

BGISEQ500和ILLUMINA数据的reads ID的差异对分析的影响待确定

Exception in thread "main" htsjdk.samtools.SAMException: Value was put into PairInfoMap more than once. 1: RGID_170523_X167_FCHKL23ALXX_L8_HUMrskEAAAAAAA-13:ST-E00167:8:2103:23155

处理BGISEQ500数据时遇到的报错

ERROR MESSAGE: SAM/BAM file SAMFileReader{/path/lane.dedup.bam} is malformed: BAM file has a read with mismatching number of bases and base qualities. Offender: CL100015487L2C006R076_221351 [1 bases] [0 quals]. You can use --defaultBaseQualities to assign a default base quality for all reads, but this can be dangerous in you don't know what you are doing.

查看bam文件发现有一条read长度为一个碱基，但碱基质量为“*”，这样的reads需要提前过滤掉

CL100015487L2C006R076_221351 117 chr1 248458064 0 * = 248458064 0 A * PG:Z:MarkDuplicates RG:Z:RGID_CL100015487_L02_1 AS:i:0 XS:i:0