bcftools 설치하기

안녕하세요

한주현입니다

오늘은 bcftools 설치에 대하여 알아보겠습니다

참조 URL

http://www.htslib.org/doc/bcftools.html

http://www.htslib.org/download/

다음 URL에 들어가시거나

http://www.htslib.org/download/

또는 제가 아래에 준비한 링크를 직접 받으셔도 됩니다

다운로드 링크

https://github.com/samtools/bcftools/releases/download/1.3.1/bcftools-1.3.1.tar.bz2

이제 본격적으로 설치해보죠..

1) 압축해제

$ tar xf bcftools-1.3.1.tar.bz2

2) 설치

$ make

$ make prefix=경로지정 install

설치과정

cd htslib-1.3.1 && make config.h
make[1]: Entering directory `/home/jhan/Downloads/bcftools-1.3.1/htslib-1.3.1'
echo '/* Empty config.h generated by Makefile */' > config.h
make[1]: Leaving directory `/home/jhan/Downloads/bcftools-1.3.1/htslib-1.3.1'
cd htslib-1.3.1 && make lib-static
make[1]: Entering directory `/home/jhan/Downloads/bcftools-1.3.1/htslib-1.3.1'
gcc -g -Wall -O2 -I.  -c -o kfunc.o kfunc.c
gcc -g -Wall -O2 -I.  -c -o knetfile.o knetfile.c
...

<생략>

...

install -p bcftools plot-vcfstats vcfutils.pl plugins/color-chrs.pl /home/jhan/etc/bcftools-1.3.1/bin
install -p -m 644 doc/bcftools.1 /home/jhan/etc/bcftools-1.3.1/share/man/man1
install -p plugins/*.so /home/jhan/etc/bcftools-1.3.1/libexec/bcftools

확인

$ pwd

/home/jhan/etc/bcftools-1.3.1/bin

$ ls -l

-rwxr-xr-x 1 jhan jhan 4828213  3월 14 11:35 bcftools
-rwxr-xr-x 1 jhan jhan   16947 10월  2  2015 color-chrs.pl
-rwxr-xr-x 1 jhan jhan   81438  2월 20  2016 plot-vcfstats
-rwxr-xr-x 1 jhan jhan   18199  8월 14  2014 vcfutils.pl
$

완료

$ bcftools

Program: bcftools (Tools for variant calling and manipulating VCFs and BCFs)
Version: 1.3.1 (using htslib 1.3.1)

Usage:   bcftools [--version|--version-only] [--help] <command> <argument>

Commands:

 -- Indexing
    index        index VCF/BCF files

 -- VCF/BCF manipulation
    annotate     annotate and edit VCF/BCF files
    concat       concatenate VCF/BCF files from the same set of samples
    convert      convert VCF/BCF files to different formats and back
    isec         intersections of VCF/BCF files
    merge        merge VCF/BCF files files from non-overlapping sample sets
    norm         left-align and normalize indels
    plugin       user-defined plugins
    query        transform VCF/BCF into user-defined formats
    reheader     modify VCF/BCF header, change sample names
    view         VCF/BCF conversion, view, subset and filter VCF/BCF files

 -- VCF/BCF analysis
    call         SNP/indel calling
    consensus    create consensus sequence by applying VCF variants
    cnv          HMM CNV calling
    filter       filter VCF/BCF files using fixed thresholds
    gtcheck      check sample concordance, detect sample swaps and contamination
    roh          identify runs of autozygosity (HMM)
    stats        produce VCF/BCF stats

 Most commands accept VCF, bgzipped VCF, and BCF with the file type detected
 automatically even when streaming from a pipe. Indexed VCF and BCF will work
 in all situations. Un-indexed VCF and BCF and streams will work in most but
 not all situations.

이상으로 bcftools 설치에 대하여 알아보았습니다

그럼 다음에 봐요~