Understanding bcftools command

Understanding bcftools command

1

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 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


filter


merge


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