samtools view 和 sort

最新推荐文章于 2023-07-25 12:41:03 发布

wangshuo0782

最新推荐文章于 2023-07-25 12:41:03 发布

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分类专栏：生信技能学习-R

本文链接：https://blog.csdn.net/wangshuo0782/article/details/104495056

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Samtools的view命令用于转换文件格式，按header或reads名称排序SAM文件。可以设置输出BAM、CRAM格式，过滤reads，选择特定区域等。而sort命令则对SAM或BAM文件按read name或位置排序，支持多线程和自定义内存设置。

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前者转化文件格式，后者将sam（比对地图）按照header位置或者reads名字排序，一般默认是位置。

下面引用其他人的笔记

samtools view

Usage: samtools view [options] <in.bam>|<in.sam>|<in.cram> [region ...]

Options:
-b output BAM
-C output CRAM (requires -T)
-1 use fast BAM compression (implies -b)
-u uncompressed BAM output (implies -b)
-h include header in SAM output
-H print SAM header only (no alignments)
-c print only the count of matching records
-o FILE output file name [stdout]
-U FILE output reads not selected by filters to FILE [null]
-t FILE FILE listing reference names and lengths (see long help) [null]
-L FILE only include reads overlapping this BED FILE [null]
-r STR only include reads in read group STR [null]
-R FILE only include reads with read group listed in FILE [null]
-q INT only include reads with mapping quality >= INT [0]
-l STR only include reads in library STR [null]
-m INT only include reads with number of CIGAR operations consuming
query sequence >= INT [0]
-f INT only include reads with all of the FLAGs in INT present [0]
-F INT only include reads with none of the FLAGS in INT present [0]
-G INT only EXCLUDE reads with all