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