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Hi,
unless I'm wrong --mark-sites in bcftools annotate ignores the parameters --min-overlap.
The Flag is always added event if the overlap isn't large enough.
In my test there are 3572 variants with or without --min-overlap "0.8:0.8"
./bcftools annotate --mark-sites +IN_DGV --min-overlap "0.8:0.8" -a dgv.bed.gz -h dgv.header.txt -c 'CHROM,POS,END,DGV' in.bcf |\
./bcftools view -G --no-header | grep IN_DGV -c
3572
./bcftools annotate --mark-sites +IN_DGV -a dgv.bed.gz -h dgv.header.txt -c 'CHROM,POS,END,DGV' in.bcf |\
./bcftools view -G --no-header | grep IN_DGV -c
3572
but there are only 545 variants overlaping the annotations.
./bcftools annotate --mark-sites +IN_DGV --min-overlap "0.8:0.8" -a dgv.bed.gz -h dgv.header.txt -c 'CHROM,POS,END,DGV' in.bcf |\
./bcftools view -G --no-header | grep -c 'DGV='
545
same command without min-overlap
./bcftools annotate --mark-sites +IN_DGV -a dgv.bed.gz -h dgv.header.txt -c 'CHROM,POS,END,DGV' in.bcf |\
./bcftools view -G --no-header | grep -c 'DGV='
3572
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