Comments (3)
Hi there! The final VCF includes coverage information on both alleles, so you could simply set a filter on that? (Clockwork does not delete any VCF rows, it simply marks them in the FILTER column). @martinghunt , what is the default min depth?
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Default depth filter is 2. Like @iqbal-lab says, the VCF has everything anyway so is easiest to re-filter the VCF file.
The filters are described here:
https://github.com/iqbal-lab-org/minos/wiki/Minos-in-single-sample-mode#call-filters
The filter options are not exposed by the clockwork variant call pipeline. If you really wanted, you could rerun the final minos command but add in your own command line options to minos (clockwork uses the default minos options).
from clockwork.
Thank you so much
from clockwork.
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