Hi,
http://bioinformatics.oxfordjournals.org/content/27/21/2987.full
The above paper does not explicitly mention which commands of samtools
the paper is for. My guess is mpileup. Is it so? Are there other
commands of samtools related with this paper? Thanks.
Program: samtools (Tools for alignments in the SAM format)
Version: 1.0 (using htslib 1.0)
Usage: samtools <command> [options]
Commands:
-- indexing
faidx index/extract FASTA
index index alignment
-- editing
calmd recalculate MD/NM tags and '=' bases
fixmate fix mate information
reheader replace BAM header
rmdup remove PCR duplicates
targetcut cut fosmid regions (for fosmid pool only)
-- file operations
bamshuf shuffle and group alignments by name
cat concatenate BAMs
merge merge sorted alignments
mpileup multi-way pileup
sort sort alignment file
split splits a file by read group
bam2fq converts a BAM to a FASTQ
-- stats
bedcov read depth per BED region
depth compute the depth
flagstat simple stats
idxstats BAM index stats
phase phase heterozygotes
stats generate stats (former bamcheck)
-- viewing
flags explain BAM flags
tview text alignment viewer
view SAM<->BAM<->CRAM conversion
--
Regards,
Peng
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