use gnomad in calculation of max_aaf_all
MODIFY
gemini/gemini_load_chunk.py
gemini/gemini_load_chunk.py
@@ -737,7 +737,15 @@ class GeminiLoader(object):
variant['aaf_adj_exac_amr'],
variant['aaf_adj_exac_eas'],
variant['aaf_adj_exac_nfe'],
- variant['aaf_adj_exac_sas'])
+ variant['aaf_adj_exac_sas'],
+
+ variant['aaf_gnomad_afr'],
+ variant['aaf_gnomad_amr'],
+ variant['aaf_gnomad_eas'],
+ variant['aaf_gnomad_nfe'],
+ variant['aaf_gnomad_sas'],
+
+ )
variant.update(self._extra_empty)
return variant, variant_impacts, extra_fields

MODIFY
test/test-query.sh
test/test-query.sh
@@ -774,11 +774,12 @@ echo "0.0 -1.0 -1.0 -1.0 -1.0 -1.0 -1.0 -1.0 0.0 0.0 0.0 0.0 0.0
-1.0 -1.0 -1.0 -1.0 -1.0 -1.0 -1.0 -1.0 -1.0 -1.0 -1.0 -1.0 -1.0
-1.0 -1.0 -1.0 -1.0 -1.0 -1.0 -1.0 -1.0 -1.0 -1.0 -1.0 -1.0 -1.0
0.996 -1.0 -1.0 0.9164 0.996 0.9233 0.6687 0.9364 -1.0 -1.0 -1.0 -1.0 -1.0
-0.98275862069 -1.0 -1.0 -1.0 -1.0 -1.0 -1.0 -1.0 0.292253521127 0.631578947368 0.98275862069 0.833928571429 0.866379310345
+0.998260365323 -1.0 -1.0 -1.0 -1.0 -1.0 -1.0 -1.0 0.292253521127 0.631578947368 0.98275862069 0.833928571429 0.866379310345
0.0497 0.0457067757009 0.003663003663 0.036 0.003 0.0153 0.0015 0.0497 0.00255297421496 0.00804493017608 0.0 0.0405799922149 0.00488782051282
-0.999403625954 0.88742933156 0.544101123596 -1.0 -1.0 -1.0 -1.0 -1.0 0.594155844156 0.950725980846 0.999403625954 0.971647095179 0.983191249799
+0.999461013295 0.88742933156 0.544101123596 -1.0 -1.0 -1.0 -1.0 -1.0 0.594155844156 0.950725980846 0.999403625954 0.971647095179 0.983191249799
0.280445372303 0.136133389616 0.0213645761544 0.0418 0.001 0.045 0.0045 0.1034 0.0217391304348 0.118834080717 0.0 0.280445372303 0.154037886341
0.0 -1.0 -1.0 -1.0 -1.0 -1.0 -1.0 -1.0 0.0 0.0 0.0 0.0 0.0" > exp
+
gemini query -q "select max_aaf_all,aaf_esp_ea, aaf_esp_aa, aaf_1kg_amr, aaf_1kg_eas, \
aaf_1kg_sas,aaf_1kg_afr,aaf_1kg_eur,aaf_adj_exac_afr,aaf_adj_exac_amr,aaf_adj_exac_eas, \
aaf_adj_exac_nfe,aaf_adj_exac_sas from variants limit 10" test.query.db > obs

use gnomad in calculation of max_aaf_all