Entering edit mode
7 weeks ago
alex.blakes • 0
I am trying to extract median DP values, across samples, from each line of a multi-sample VCF. (The DP for each individual sample is given in the FORMAT columns. There are ~400,000 samples for most sites)
I know I can filter on the median DP values, (e.g. with bcftools query -i MEDIAN(DP)>30 )
But I can't find a way to actually extract and print the median value.
I thought I would be able to do this with something like: bcftools query -f MEDIAN(DP)
But no dice!
I'd be grateful for any suggestions.