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[转载]SAMtool bitwise flag meaning explained

已有 670 次阅读 2018-9-30 23:28 |个人分类:科研经验|系统分类:科研笔记|关键词:学者|文章来源:转载

 

If you got samflags and want to know their meaning quickly then you can check their meaning interactively following this link. You type in a flag and will get the answer at Piacrd official site.

You can also look up the meaning of samflags in a pdf file sam_output in pdf. Or it looks like this:


For example, you can use following cmd to abstract the reads which are self mapped but mated reads are not mapped: 

samtools view -f 8 -F 4 ***.bam

Also, you can use following cmd to abstract the reads which are not self mapped but mated reads are mapped: 

samtools view -f 4 -F 8 ***.bam



Raw text: https://ppotato.wordpress.com/2010/08/25/samtool-bitwise-flag-paired-reads/

 





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