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Understanding bcftools command

I need to perform the following action to combine multiple vcf files into one

BCF=/path_to_bcftools
export BCFTOOLS_PLUGINS=$BCF/plugins
DIR=/path_to_normal_vcf_file
$BCF/bcftools merge -m all -f PASS,. --force-samples $DIR/*.vcf.gz |\
$BCF/bcftools plugin fill-AN-AC |\
$BCF/bcftools filter -i 'SUM(AC)>1' > panel_of_normal.vcf

I don't have access to command-line bcftools, and since this is a one-time need I plan to use https://usegalaxy.org/ BUT I'm not clear how to implement the last two steps i.e.

$BCF/bcftools plugin fill-AN-AC |\
$BCF/bcftools filter -i 'SUM(AC)>1' > panel_of_normal.vcf

Can I perform this entire command using Galaxy, and if so, can anyone guide me on how to carry out the last two lines?

Thank you

bcftools merge filter
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updated by Ram Ram • written by rtho • rtho

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written by Ram Ram

1 answer

If you look at the BCF tools in Galaxy you will see that each that you list can be run, and can be filled in with the appropriate parameters.

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written by Istvan Albert Istvan Albert

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