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ivar variants: reducing q-score threshold results in high P-value for deletion #96
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Seeing the same issue with the 6p deletion When setting
When setting
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Dear @gkarthik ,
I tried to change the option
-q
inivar variants
to values below the default 20 and discovered a problem with calling deletions once the q-score threshold is set to a value below 10.My data is SARS-CoV2 and the deletion in question is the del69/70 in spike at position 21764.
With this command I tried all values for
-q
from 0 to 20:The output for position 21764 is:
For
-q 10
and above, the variant is found with P-value = 0, and for-q 9
and below, it is not found with P-value = 1.The main difference between the files is that the column ALT_QUAL takes on exactly the value set for
-q
, probably because ofivar/src/allele_functions.cpp
Line 90 in ce1490a
This value is then used here
ivar/src/call_variants.cpp
Line 138 in ce1490a
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