【6.1.2.2】bcftools

一、安装

wget -c https://github.com/samtools/bcftools/releases/download/1.15.1/bcftools-1.15.1.tar.bz2
tar xjvf bcftools-1.15.1.tar.bz2


cd bcftools-1.15.1
make 
make install 

vim /etc/profile

二、用法

• https://samtools.github.io/bcftools/howtos/variant-calling.html
• https://samtools.github.io/bcftools/bcftools.html#mpileup

用法：

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
    head         view VCF/BCF file headers
    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
    sort         sort VCF/BCF file
    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
    csq          call variation consequences
    filter       filter VCF/BCF files using fixed thresholds
    gtcheck      check sample concordance, detect sample swaps and contamination
    mpileup      multi-way pileup producing genotype likelihoods
    roh          identify runs of autozygosity (HMM)
    stats        produce VCF/BCF stats

 -- Plugins (collection of programs for calling, file manipulation & analysis)
    38 plugins available, run "bcftools plugin -lv" to see a complete list

四、报错

4.1 报错：

make[1]: Entering directory `/data/software/bcftools-1.15.1/htslib-1.15.1'
gcc -g -Wall -O2 -fvisibility=hidden -I.  -c -o hfile_libcurl.o hfile_libcurl.c
hfile_libcurl.c:47:10: fatal error: curl/curl.h: No such file or directory
   47 | #include <curl/curl.h>
      |          ^~~~~~~~~~~~~
compilation terminated.
make[1]: *** [hfile_libcurl.o] Error 1
make[1]: Leaving directory `/data/software/bcftools-1.15.1/htslib-1.15.1'
make: *** [htslib-1.15.1/hts-object-files] Error 2

解决办法：

sudo yum install libcurl-dev libcurl-devel

参考资料