Hello,

I'm trying to remove variants that are within 1000 bp of contig ends from by bcf file using BCFtools. I know how to remove those from the beggining:

bcftools filter -i 'POS>1000' my.bcf -o my_filtered.bcf

...but not ends. I thought about adding a column of contig lengths to my vcf when calling with BCFtools mpileup/call, and doing something like:

bcftools filter -i 'POS>1000 && POS<END-1000' my.bcf -o my_filtered.bcf

but I'm unable to produce the 'END' field. I'd appreciate any help.