【提示】本文写作命令为：abysw blog arm服务器安装samtools
华为的服务做的还算可以，常用的生物信息分析软件都做了适配。
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下载所需版本samtools （github）
解压
编译
make all all-htslib
make install install-htslib
Program: samtools (Tools for alignments in the SAM format)
Version: 1.7 (using htslib 1.7)
Usage: samtools
Commands:
– Indexing
dict create a sequence dictionary file
faidx index/extract FASTA
index index alignment
– Editing
calmd recalculate MD/NM tags and ‘=’ bases
fixmate fix mate information
reheader replace BAM header
targetcut cut fosmid regions (for fosmid pool only)
addreplacerg adds or replaces RG tags
markdup mark duplicates
– File operations
collate 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
quickcheck quickly check if SAM/BAM/CRAM file appears intact
fastq converts a BAM to a FASTQ
fasta converts a BAM to a FASTA
– Statistics
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
depad convert padded BAM to unpadded BAM