How To Install bcftools on CentOS 8

bcftools is Tools for genomic variant calling and manipulating VCF/BCF files

Introduction

In this tutorial we learn how to install bcftools on CentOS 8.

What is `bcftools`

BCFtools is a set of utilities that manipulate genomic variant calls in the Variant Call Format (VCF) and its binary counterpart (BCF). All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed. (This BCFtools includes the polysomy subcommand, which is implemented using the GNU Scientific Library. Hence this package is licensed according to the GNU General Public License, rather than the MIT license used when BCFtools is built without the polysomy subcommand.)

We can use yum or dnf to install bcftools on CentOS 8. In this tutorial we discuss both methods but you only need to choose one of method to install bcftools.

Install bcftools on CentOS 8 Using dnf

Update yum database with dnf using the following command.

sudo dnf makecache --refresh

The output should look something like this:

CentOS Linux 8 - AppStream                                       43 kB/s | 4.3 kB     00:00    
CentOS Linux 8 - BaseOS                                          65 kB/s | 3.9 kB     00:00    
CentOS Linux 8 - ContinuousRelease                               43 kB/s | 3.0 kB     00:00    
CentOS Linux 8 - Extras                                          23 kB/s | 1.5 kB     00:00    
CentOS Linux 8 - FastTrack                                       40 kB/s | 3.0 kB     00:00    
CentOS Linux 8 - HighAvailability                                36 kB/s | 3.9 kB     00:00    
CentOS Linux 8 - Plus                                            24 kB/s | 1.5 kB     00:00    
CentOS Linux 8 - PowerTools                                      50 kB/s | 4.3 kB     00:00    
Extra Packages for Enterprise Linux Modular 8 - x86_64           13 kB/s | 9.2 kB     00:00    
Extra Packages for Enterprise Linux 8 - x86_64                   24 kB/s | 8.5 kB     00:00    
Metadata cache created.

After updating yum database, We can install bcftools using dnf by running the following command:

sudo dnf -y install bcftools

Install bcftools on CentOS 8 Using yum

Update yum database with yum using the following command.

sudo yum makecache --refresh

The output should look something like this:

CentOS Linux 8 - AppStream                                       43 kB/s | 4.3 kB     00:00    
CentOS Linux 8 - BaseOS                                          65 kB/s | 3.9 kB     00:00    
CentOS Linux 8 - ContinuousRelease                               43 kB/s | 3.0 kB     00:00    
CentOS Linux 8 - Extras                                          23 kB/s | 1.5 kB     00:00    
CentOS Linux 8 - FastTrack                                       40 kB/s | 3.0 kB     00:00    
CentOS Linux 8 - HighAvailability                                36 kB/s | 3.9 kB     00:00    
CentOS Linux 8 - Plus                                            24 kB/s | 1.5 kB     00:00    
CentOS Linux 8 - PowerTools                                      50 kB/s | 4.3 kB     00:00    
Extra Packages for Enterprise Linux Modular 8 - x86_64           13 kB/s | 9.2 kB     00:00    
Extra Packages for Enterprise Linux 8 - x86_64                   24 kB/s | 8.5 kB     00:00    
Metadata cache created.

After updating yum database, We can install bcftools using yum by running the following command:

sudo yum -y install bcftools

How To Uninstall bcftools on CentOS 8

To uninstall only the bcftools package we can use the following command:

sudo dnf remove bcftools

bcftools Package Contents on CentOS 8

/usr/bin/bcftools
/usr/bin/color-chrs.pl
/usr/bin/guess-ploidy.py
/usr/bin/plot-roh.py
/usr/bin/plot-vcfstats
/usr/bin/run-roh.pl
/usr/bin/vcfutils.pl
/usr/lib/.build-id
/usr/lib/.build-id/03
/usr/lib/.build-id/03/fc66073bf06c2b7007967b1105450c0bd7ed9b
/usr/lib/.build-id/08
/usr/lib/.build-id/08/7fd1af48e6fa09e2c1cfabc8ca45ad44695f72
/usr/lib/.build-id/25
/usr/lib/.build-id/25/81eaeeb8f130c84b31680c6f660b7d9f654577
/usr/lib/.build-id/33
/usr/lib/.build-id/33/3ba7b4e7c89835cf5e111a704251289fb98c20
/usr/lib/.build-id/34
/usr/lib/.build-id/34/7c97aef1a3e1658f1f48338f07f8a6853ade11
/usr/lib/.build-id/39
/usr/lib/.build-id/39/5abe1b62edab720ad9a693eba6744b6bc9de36
/usr/lib/.build-id/3a
/usr/lib/.build-id/3a/9792436e71b790a2a9fc2fb94d687f18ac01b3
/usr/lib/.build-id/40
/usr/lib/.build-id/40/c45bf562c041c523ba291eedd3a0b1094f43ce
/usr/lib/.build-id/42
/usr/lib/.build-id/42/9856e64eaa279d1019ebb1e2a9c0e2b3589ff4
/usr/lib/.build-id/43
/usr/lib/.build-id/43/b9fbc2c6f92df254d20c86e572c8228466c7b3
/usr/lib/.build-id/55
/usr/lib/.build-id/55/398a707bfc77648a9e3607b908dbb638e5b6d2
/usr/lib/.build-id/71
/usr/lib/.build-id/71/091aab2b0ca7bf0312373acaccb432b597a65a
/usr/lib/.build-id/78
/usr/lib/.build-id/78/076b4a913aed2acf45e08a289740ef26819781
/usr/lib/.build-id/7f
/usr/lib/.build-id/7f/da9a735f138aa7f9e23bc9d3a49b75c21dab12
/usr/lib/.build-id/81
/usr/lib/.build-id/81/bf050438cf416987f988a5a567854306653987
/usr/lib/.build-id/8a
/usr/lib/.build-id/8a/258842ca86cc14a8a1bd4402605d30a5f8359e
/usr/lib/.build-id/8e
/usr/lib/.build-id/8e/2c6f05e51fcaaee3312bd3b2a80ff497085f96
/usr/lib/.build-id/90
/usr/lib/.build-id/90/40045584b665ddfca61eda0784d1a314e5f479
/usr/lib/.build-id/b5
/usr/lib/.build-id/b5/73edfd60c90bc4b5459b02e9a59d0ef68d3fa6
/usr/lib/.build-id/b6
/usr/lib/.build-id/b6/2454ec126de2a4183c71341af3b1461acad7a4
/usr/lib/.build-id/b6/8c382293e91582bad8a26255b29a0ceed98885
/usr/lib/.build-id/bc
/usr/lib/.build-id/bc/f1c2f29152c5d84d84d62ac170c43ce235b691
/usr/lib/.build-id/bf
/usr/lib/.build-id/bf/6d589e0d228d8245c5e2b2d0dd1d2e236aba7f
/usr/lib/.build-id/c8
/usr/lib/.build-id/c8/2ae2ad86c6b34d00702898c1a03fe7dcf7f600
/usr/lib/.build-id/cc
/usr/lib/.build-id/cc/d5cba35944363c4daa8a36f811c9e4961ce765
/usr/lib/.build-id/d6
/usr/lib/.build-id/d6/f73e0cd62189b5762cce88aa2187a1c2e2fd72
/usr/lib/.build-id/e7
/usr/lib/.build-id/e7/6a046ca65728a8be0bd711d7fb44aa82d7c637
/usr/lib/.build-id/e9
/usr/lib/.build-id/e9/1cebb68c8c8430778cabb8f700ff53585ff78d
/usr/lib/.build-id/fb
/usr/lib/.build-id/fb/c2f19a495a760c53994c3860fbbf56dd8dbd54
/usr/libexec/bcftools
/usr/libexec/bcftools/GTisec.so
/usr/libexec/bcftools/GTsubset.so
/usr/libexec/bcftools/ad-bias.so
/usr/libexec/bcftools/af-dist.so
/usr/libexec/bcftools/check-ploidy.so
/usr/libexec/bcftools/check-sparsity.so
/usr/libexec/bcftools/color-chrs.so
/usr/libexec/bcftools/contrast.so
/usr/libexec/bcftools/counts.so
/usr/libexec/bcftools/dosage.so
/usr/libexec/bcftools/fill-AN-AC.so
/usr/libexec/bcftools/fill-from-fasta.so
/usr/libexec/bcftools/fill-tags.so
/usr/libexec/bcftools/fixploidy.so
/usr/libexec/bcftools/fixref.so
/usr/libexec/bcftools/frameshifts.so
/usr/libexec/bcftools/guess-ploidy.so
/usr/libexec/bcftools/impute-info.so
/usr/libexec/bcftools/isecGT.so
/usr/libexec/bcftools/mendelian.so
/usr/libexec/bcftools/missing2ref.so
/usr/libexec/bcftools/prune.so
/usr/libexec/bcftools/setGT.so
/usr/libexec/bcftools/smpl-stats.so
/usr/libexec/bcftools/split.so
/usr/libexec/bcftools/tag2tag.so
/usr/libexec/bcftools/trio-stats.so
/usr/libexec/bcftools/trio-switch-rate.so
/usr/share/doc/bcftools
/usr/share/doc/bcftools/AUTHORS
/usr/share/doc/bcftools/NEWS
/usr/share/licenses/bcftools
/usr/share/licenses/bcftools/LICENSE
/usr/share/man/man1/bcftools.1.gz

References

bcftools website

Summary

In this tutorial we learn how to install bcftools on CentOS 8 using yum and dnf.