Hi- I’m trying to merge several vcf files with bcftools merge using Galaxy. The command line I need to use includes these two lines, and I don’t understand where and how to input plugin fill-AN-AC and filter -i 'SUM(AC)>1’
$BCF/bcftools plugin fill-AN-AC |
$BCF/bcftools filter -i ‘SUM(AC)>1’ > panel_of_normal.vcf
I tried adding ‘SUM(AC)>1’ under ‘Info Rules’ but that caused an error (leaving that input empty did allow the job to complete, but of course it misses out this part of the command).
Can anyone help me to reproduce these parameters in Galaxy?