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3.1 years 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
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