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Create a issue in ivar - indels #16
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Describe the bugWe have observed that
Position 28247 has a well supported deletion (nearly 70000x coverage) and
This variant should be included in the consensus according to our quality criteria (variants with an AF > 0.75). Therefore, the AF is overestimated due to the misscalculation in the variant depth (because of the deletion).
Other variant callers such us Varscan detect this variant with an AF << 0.25 because the depth of that position is calculated taking into account the deletion reads. Thus, the AF differs from ivar variants. Expected behaviorWe might suggest that This issue may be related to #79, #83, #85, #103 To ReproduceRun ivar variants with these params:
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Better comprehension and need data to reproduce the issue. |
Done #126 |
Create a issue to examine the ivar performance in indels
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