Understanding bcftools command
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10 months ago
rtho ▴ 20

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 • 787 views
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10 months ago

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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