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Added two annotations from v3 (absent from v2) to annotations hists c… #181

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Merged
lfrancioli merged 2 commits into from
Mar 5, 2020
Merged

Added two annotations from v3 (absent from v2) to annotations hists c… #181

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d1b1056
Added two annotations from v3 (absent from v2) to annotations hists c…
lfrancioli Mar 3, 2020
636f47c
Corrected bugs in get_annotations_hists
lfrancioli Mar 3, 2020
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4 changes: 2 additions & 2 deletions gnomad/utils/annotations.py
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Original file line number Diff line number Diff line change
Expand Up @@ -964,10 +964,10 @@ def get_annotations_hists(
# Check all fields in ht.info and create histograms if they are in annotations_hists dict
return {
field: hl.agg.hist(
hl.log10(ht[field]) if field in log10_annotations else ht[field],
hl.log10(ht.info[field]) if field in log10_annotations else ht.info[field],
start,
end,
bin,
bins,
)
for field, (start, end, bins) in annotations_hists.items()
if field in ht.row.info
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2 changes: 2 additions & 0 deletions gnomad/utils/constants.py
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Original file line number Diff line number Diff line change
Expand Up @@ -71,6 +71,7 @@
'FS': (0, 50, 50), # NOTE: in 2.0.2 release this was on (0,20)
'InbreedingCoeff': (-0.25, 0.25, 50),
'MQ': (0, 80, 40),
'RAW_MQ': (2, 13, 33),
'MQRankSum': (-15, 15, 60),
'QD': (0, 40, 40),
'ReadPosRankSum': (-15, 15, 60),
Expand All @@ -79,6 +80,7 @@
'ClippingRankSum': (-5, 5, 40),
'DP': (1, 9, 32), # NOTE: in 2.0.2 release this was on (0,8)
'VQSLOD': (-30, 30, 60), # NOTE: in 2.0.2 release this was on (-20,20)
'AS_VQSLOD': (-30, 30, 60),
'rf_tp_probability': (0, 1, 50),
'pab_max': (0, 1, 50)
}