实验记录 | Lofreq的安装

参考链接：http://csb5.github.io/lofreq/
这篇文章中有介绍若干安装lofreq的方法，其中使用conda安装则最为简单，因此，本文使用conda进行Lofreq的安装。
参考链接：https://anaconda.org/bioconda/lofreq
conda install -c bioconda lofreq
安装过程非常顺利。
检验是否安装成功：
lofreq

屏幕显示：

Fast and sensitive inference of SNVs and indels
Usage: lofreq [options]
Main Commands:
call : Call variants
call-parallel : Call variants in parallel
somatic : Call somatic variants
Preprocessing Commands
viterbi : Viterbi realignment
indelqual : Insert indel qualities
alnqual : Insert base and indel alignment qualities
Other Commands:
checkref : Check that reference fasta and BAM file match
filter : Filter variants in VCF file
uniq : Test whether variants predicted in only one sample really are unique
plpsummary : Print pileup summary per position
vcfset : VCF set operations
version : Print version info
Samtools Clones:
faidx : Create index for fasta file
index : Create index for BAM file
idxstats : Print stats for indexed BAM file
Extra Tools (if installed):
vcfplot : Plot VCF statistics

安装成功。