Unexpected sites after filtering variants
I have filtered my call set with
VariantFiltration using the following filter:
QD < 2.0 || FS > 60.0 || MQ < 40.0 || MQRankSum < -12.5 || ReadPosRankSum < -8.0
Then I extracted all sites (including filtered records) in the form of a table with
Checking the ranges of each annotation that passed the filter (labeled as
PASS in field
FILTER), I see an unexpected behavior for
MQ: some of the records (
PASS) are below 40.
For the rest of the annotations, the ranges appear as expected, as shown below:
QD: 2.000 (min), 46.37 (max) FS: 0.000 (min), 60.00 (max) MQ: 0.850 (min), 725.20 (max) MQRankSum: -12.500 (min), 26.43 (max) ReadPosRankSum: -7.818 (min), 30.39 (max)
However, the amount of unexpected records (
MQ < 40.0) were only 95 (out of 13126298).
I am sure I am missing something in my interpretation, but the way I understand this,
MQ should have a minimum larger or equal 40 for those records that passed.
Could you please help me to make sense of this?