What is the difference between the -T option and -f option used with Illumina's hap.py (vcf comparison tool)?
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7.5 years ago
Curious3 • 0

It seems like the hap.py manual does not have a good example to explain the difference between using the -f option versus -T option. I used the -f option with a confident bed file but looks like the algorithm may not be using the bed file the way I thought it would. I would like all the variants in query vcf file that are compared with the truth vcf file to fall in the bed file regions provided. Could anyone help clarify?

Thanks!

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