More on SAMTools
Command Line Usage:
samtools <command> [options]
For a list of all available tools, type
samtools --help
Some common commands are:
| view | SAM< – >BAM< – > CRAM 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 |
| targetcut | cut fosmid regions (for fosmid pool only) |
| phase | phase heterozygotes |