Complete Guide: Installing dindel on Ubuntu 20.10 (Groovy Gorilla) 2024

1. Install "dindel" package

Here is a brief guide to show you how to install dindel on Ubuntu 20.10 (Groovy Gorilla)


    
        
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                sudo apt update
            
                    
    
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                sudo apt install
            
                        
                dindel
            
                    
    
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2. Uninstall "dindel" package

This tutorial shows how to uninstall dindel on Ubuntu 20.10 (Groovy Gorilla):


    
        
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                sudo apt remove
            
                        
                dindel
            
                    
    
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                sudo apt autoclean && sudo apt autoremove
            
                    
    
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3. Information about the dindel package on Ubuntu 20.10 (Groovy Gorilla)

Package: dindel
Architecture: amd64
Version: 1.01-wu1-3+dfsg-1build1
Priority: optional
Section: universe/science
Origin: Ubuntu
Maintainer: Ubuntu Developers
Original-Maintainer: Debian Med Packaging Team
Bugs: https://bugs.launchpad.net/ubuntu/+filebug
Installed-Size: 1082
Depends: libboost-program-options1.71.0, libc6 (>= 2.29), libgcc-s1 (>= 3.0), libstdc++6 (>= 9), zlib1g (>= 1:1.2.3.3)
Filename: pool/universe/d/dindel/dindel_1.01-wu1-3+dfsg-1build1_amd64.deb
Size: 369596
MD5sum: 0b927a3da631954443d3278b5ec04be4
SHA1: 7baa6edf2a84ad1c1b35d4c29c7b3269e39b12a2
SHA256: abfb5972bf5cb0ef0ae633bb608e0ed62fb9719a31eb2545b51a140df744cc89
SHA512: b57a7043221af3e039d510e765ebf80bdc9805beb0aa1051a65f969f6aa2192e7f53209a03d26d94ce35ea4bf78c65aea4fadebfb1659b88ecde2da523caf5d6
Homepage: https://github.com/genome/dindel-tgi
Description-en: determines indel calls from short-read data
Dindel is a program for calling small indels from short-read sequence
data ('next generation sequence data'). It currently is designed to
handle only Illumina data.
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Dindel requires a BAM file containing the read-alignments as input. It
then extracts candidate indels from the BAM file, and realigns the reads
to candidate haplotypes consisting of these candidate indels. If there
is sufficient evidence for an alternative haplotype to the reference,
it will call an indel.
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It is possible to test indels discovered with other methods using Dindel,
for instance longer indels obtained through assembly methods. Dindel
will then realign both mapped and unmapped reads to see if the candidate
indel is supported by the reads.
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Dindel outputs both genotype likelihoods and includes a script to
convert these to a VCF file with indel and SNP calls.
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There is basic support for outputting realigned BAM files for each
realignment-window. These realigned BAM files can be used to call SNPs
near (candidate) indels.
Description-md5: 0dc5a418bf794b531b75553abaea6408