3.1 view命令基础功能
$ samtools view
Usage: samtools view [options] <in.bam>|<in.sam>|&am> [region ...] Output options:
-b, --bam Output BAM
-C, --cram Output CRAM (requires -T)
-1, --fast U fast BAM compression (implies --bam)
-u, --uncompresd Uncompresd BAM output (implies --bam)
-h, --with-header Include header in SAM output
-H, --header-only Print SAM header only (no alignments)
--no-header Print SAM alignment records only [default]
西梅的功效与作用-c, --count Print only the count of matching records
-
o, --output FILE Write output to FILE [standard output]
-U, --unoutput FILE, --output-unlected FILE
网名名字大全Output reads not lected by filters to FILE
-p, --unmap Set flag to UNMAP on reads not lected
then write to output file.
Input options:
-t, --fai-reference FILE FILE listing reference names and lengths
-M, --u-index U index and multi-region iterator for regions
--region[s]-file FILE U index to include only reads overlapping FILE
-X, --customized-index Expect extra index file argument after <in.bam> Filtering options (Only include in output ):
-L, --target[s]-file FILE ...overlap (BED) regions in FILE
-r, --read-group STR ...are in read group STR
-R, --read-group-file FILE ...are in a read group listed in FILE
-N, --qname-file FILE ...who read name is listed in FILE
-d, --tag STR1[:STR2] ...have a tag STR1 (with associated value STR2)
-D, --tag-file STR:FILE ...have a tag STR who value is listed in FILE
-q, --min-MQ INT ...have mapping quality >= INT精神集中
-l, --library STR ...are in library STR
-m, --min-qlen INT ...cover >= INT query bas (as measured via CIGAR) -e, --expr STR ...match the filter expression STR
-f, --require-flags FLAG ...have all of the FLAGs prent老人与海英语
-F, --excl[ude]-flags FLAG ...have none of the FLAGs prent
-G FLAG EXCLUDE reads with all of the FLAGs prent
--subsample FLOAT Keep only FLOAT fraction of templates/read pairs --subsample-ed INT Influence WHICH reads are kept in subsampling [0] -s INT.FRAC Same as --subsample 0.FRAC --subsample-ed INT Processing options:
--add-flags FLAG Add FLAGs to reads
--remove-flags FLAG Remove FLAGs from reads
怎样制作萝卜干-x, --remove-tag STR
Comma-parated read tags to strip (repeatable) [null]草字头加仕
--keep-tag STR
Comma-parated read tags to prerve (repeatable) [null].
Equivalent to "-x ^STR"
-B, --remove-B Collap the backward CIGAR operation
General options:
-?, --help Print long help, including note about region specification
-S Ignored (input format is auto-detected)
--no-PG Do not add a PG line
--input-fmt-option OPT[=VAL]
Specify a single input file format option in the form
of OPTION or OPTION=VALUE
麦片怎么做好吃-O, --output-fmt FORMAT[,OPT[=VAL]]...
Specify output format (SAM, BAM, CRAM)
--output-fmt-option OPT[=VAL]
Specify a single output file format option in the form
of OPTION or OPTION=VALUE
-
T, --reference FILE
Reference quence FASTA FILE [null]
局域网聊天-@, --threads INT
Number of additional threads to u [0]
--write-index
Automatically index the output files [off]
