libvcflib-tools error: Unable to correct problems, you have held broken packages
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Entering edit mode
2.5 years ago

Hello

I am using Ubuntu 20.04 lts. And i am trying to run a command using vcflib

> vcflib vcfallelicprimitives -m input_file > output_file

everytime it returns with this

Command 'vcflib' not found, but can be installed with:

sudo apt install libvcflib-tools

But when i try to install libvcflib-tools by

sudo apt install libvcflib-tools

i get this error

Reading package lists... Done
Building dependency tree       
Reading state information... Done
Some packages could not be installed. This may mean that you have
requested an impossible situation or if you are using the unstable
distribution that some required packages have not yet been created
or been moved out of Incoming.
The following information may help to resolve the situation:

The following packages have unmet dependencies:
 libvcflib-tools : Depends: r-cran-plyr but it is not going to be installed
                   Depends: r-cran-ggplot2 but it is not going to be installed
                   Depends: r-cran-gridbase but it is not going to be installed
E: Unable to correct problems, you have held broken packages.

I am stuck at this point and do not know what to do. Kindly help me out.

Thanks in advance

vcflib ubuntu20.04 libvcflib-tools • 1.2k views
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Entering edit mode
2.5 years ago

vcfallelicprimitives If multiple allelic primitives (gaps or mismatches) are specified in a single VCF record, split the record into multiple lines, but drop all INFO fields.

unless I'm wrong, that's the job of bcftools norm -m TYPE (followed by bcftools annotated)

-m, --multiallelics -|+TYPE     Split multiallelics (-) or join biallelics (+), type: snps|indels|both|any [both]
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Entering edit mode

Yes, but i am using vcflib tool and want to resolve the aforementioned error. Would you please guide me about that.

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