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 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?
• 46 views