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dieterich-lab / JACUSA2

New version of JACUSA -> 2.0
GNU General Public License v3.0
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Support zero depth sites #48

Open y9c opened 3 years ago

y9c commented 3 years ago

For analyzing multiple samples together, it is useful to accept sites whose depth is 0 within some samples.

Sfeng666 commented 10 months ago

For analyzing multiple samples together, it is useful to accept sites whose depth is 0 within some samples.

I agree.

It also make more sense to allow coverage = 0. Both the mapping quality (-m) and base call quality (-q) filterings allow no filtering (threshold = 0).

piechottam commented 10 months ago

I will try to incorporate -m and -q with threshold 0. A coverage of 0 requires extensive updates to how the test-statistic is calculated - I'll check this.