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本文介绍了如何利用samtools的-f /-F/-G参数从bam文件中筛选特定类型的reads。通过理解这些参数的用法，如-f用于仅输出含有特定标志的alignment，-F用于排除含有特定标志的alignment，以及-G用于排除所有含有特定标志的alignment，可以精确地提取所需数据。
解决方案
通过指定samtools view 的-f /-F/-G参数的FLAGS即可愉快的从bam中提取预期的reads
-f /-F/-G参数介绍
-f FLAG, --require-flags FLAG
Only output alignments with all bits set in FLAG present in the FLAG field. FLAG can be specified in hex by beginning with `0x' (i.e. /^0x[0-9A-F]+/), in octal by beginning with `0' (i.e. /^0[0-7]+/), as a decimal number not beginning with '0' or as a comma-separated list of flag names.
-F FLAG, --excl-flags FLAG, --exclude-flags FLAG
Do not output alignments with any bits set in FLAG present in the FLAG field. FLAG can be specified in hex by beginning with `0x' (i.e. /^0x[0-9A-F]+/), in octal by beginning with `0' (i.e. /^0[0-7]+/), as a decimal number not beginning with '0'
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