How To Install bcftools on Fedora 34
Introduction
In this tutorial we learn how to install bcftools on Fedora 34.
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 Fedora 34. In this tutorial we discuss both methods but you only need to choose one of method to install bcftools.
Install bcftools on Fedora 34 Using dnf
Update yum database with dnf using the following command.
sudo dnf makecache --refresh
The output should look something like this:
Fedora 34 - x86_64 20 kB/s | 6.6 kB 00:00
Fedora 34 openh264 (From Cisco) - x86_64 1.4 kB/s | 989 B 00:00
Fedora Modular 34 - x86_64 68 kB/s | 6.5 kB 00:00
Fedora 34 - x86_64 - Updates 3.5 kB/s | 6.2 kB 00:01
Fedora Modular 34 - x86_64 - Updates 17 kB/s | 5.9 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 Fedora 34 Using yum
Update yum database with yum using the following command.
sudo yum makecache --refresh
The output should look something like this:
Fedora 34 - x86_64 20 kB/s | 6.6 kB 00:00
Fedora 34 openh264 (From Cisco) - x86_64 1.4 kB/s | 989 B 00:00
Fedora Modular 34 - x86_64 68 kB/s | 6.5 kB 00:00
Fedora 34 - x86_64 - Updates 3.5 kB/s | 6.2 kB 00:01
Fedora Modular 34 - x86_64 - Updates 17 kB/s | 5.9 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 Fedora 34
To uninstall only the bcftools package we can use the following command:
sudo dnf remove bcftools
bcftools Package Contents on Fedora 34
/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/16
/usr/lib/.build-id/16/463c66c298550343f7bdb1548eae2b3179fe72
/usr/lib/.build-id/20
/usr/lib/.build-id/20/bf43a20d921c3b7d8e83975aace52d958b6a51
/usr/lib/.build-id/3e
/usr/lib/.build-id/3e/a72d0ddb4ae5d90c0302fda5b5fe2a08ad726f
/usr/lib/.build-id/42
/usr/lib/.build-id/42/59f603a5fbf0661826a9378848845d142ad92c
/usr/lib/.build-id/4b
/usr/lib/.build-id/4b/9a8b2cd5d640c40945ec96810b97f0aacb5d7d
/usr/lib/.build-id/4f
/usr/lib/.build-id/4f/8c185933cc298671abbbcd4b438132b808c3f2
/usr/lib/.build-id/62
/usr/lib/.build-id/62/63cea94bb9d0d99891c587e6fa4fd0045071e2
/usr/lib/.build-id/63
/usr/lib/.build-id/63/c67c670cdcc4ebe3fe1b2731b3579cca118792
/usr/lib/.build-id/64
/usr/lib/.build-id/64/6c78cfeb5f9da014e7e1d8dad38a1a7990d0af
/usr/lib/.build-id/67
/usr/lib/.build-id/67/d47c27fca7aba2fdeee1487bb7a4a83265a9ab
/usr/lib/.build-id/80
/usr/lib/.build-id/80/c34646c4c8f99b82164b702af43f3dee1a442f
/usr/lib/.build-id/86
/usr/lib/.build-id/86/3e69d2e1c8d5482892d31302e14a8149839e6b
/usr/lib/.build-id/8b
/usr/lib/.build-id/8b/374c1d4544ee5f86b1e8edeb9d57cf9a32b463
/usr/lib/.build-id/8e
/usr/lib/.build-id/8e/1ff1aeec18919b4dc0bbf1f5e376698d39118c
/usr/lib/.build-id/8f
/usr/lib/.build-id/8f/50fb763f409920a64e2491cef888b029356453
/usr/lib/.build-id/95
/usr/lib/.build-id/95/b1a2d970d07ef510db3860fd66200023f77d3e
/usr/lib/.build-id/97
/usr/lib/.build-id/97/c85adbecc9ab36f0da454aae1b56d50138c9d1
/usr/lib/.build-id/9a
/usr/lib/.build-id/9a/9a016784b5a0641d5d8b08b60d0a6ff27f6233
/usr/lib/.build-id/a2
/usr/lib/.build-id/a2/2ae8b1f8890c53c8d53f8bc7932cc17db9e8c3
/usr/lib/.build-id/a8
/usr/lib/.build-id/a8/c5e32a42e455e11ec04a21182cf6fc2bc48bf2
/usr/lib/.build-id/aa
/usr/lib/.build-id/aa/6b09f54867447a17fb83b0810f0da2d72d4068
/usr/lib/.build-id/b5
/usr/lib/.build-id/b5/57c9bc23013324032ef92f5df722488da81253
/usr/lib/.build-id/c4
/usr/lib/.build-id/c4/8160d5e90197a4b8f21acb1b22f8131b715e03
/usr/lib/.build-id/c6
/usr/lib/.build-id/c6/1326b2ae676a5ce75331fb133f07cc8de36e68
/usr/lib/.build-id/cf
/usr/lib/.build-id/cf/5964a9a432948aacc27ced1a1ecb3766490bd0
/usr/lib/.build-id/d1
/usr/lib/.build-id/d1/5db4d4d71b864120f6a4a90dc2bc88bffef459
/usr/lib/.build-id/d7
/usr/lib/.build-id/d7/56f3842d52c758cb0cadf1765ed1eaf9efb45b
/usr/lib/.build-id/f2
/usr/lib/.build-id/f2/9fe1161c51eae25b97dd03c795365007661ff0
/usr/lib/.build-id/fd
/usr/lib/.build-id/fd/66306e3acd54b5c75635dff01e61c43bfecc56
/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 Fedora 34 using yum and dnf.