samtools使用说明书.pdfVIP

Program: samtools (Tools for alignments in the SAM format) Version: 0.1.19-44428cd Usage: samtools command [options] Command: view SAM-BAM conversion sort sort alignment file mpileup multi-way pileup depth compute the depth faidx index/extract FASTA tview text alignment viewer index index alignment idxstats BAM index stats (r595 or later) fixmate fix mate information flagstat simple stats calmd recalculate MD/NM tags and = bases merge merge sorted alignments rmdup remove PCR duplicates reheader replace BAM header cat concatenate BAMs bedcov read depth per BED region targetcut cut fosmid regions (for fosmid pool only) phase phase heterozygotes bamshuf shuffle and group alignments by name ./samtools view Usage: samtools view [options] in.bam|in.sam [region1 [...]] Options: -b output BAM -h print header for the SAM output -H print header only (no alignments) -S input is SAM -u uncompressed BAM output (force -b) -1 fast compression (force -b) -x output FLAG in HEX (samtools-C specific) -X output FLAG in string (samtools-C specific) -c print only the count of matching records -B collapse the backward CIGAR operation -@ INT number of BAM compression threads [0] -L FILE output alignments overlapping the input BED FILE [null] -t FILE list of reference names and lengths (force -S) [null] -T FILE reference sequence file (force -S