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update criteria for variant filtering and annotation #47

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Merged
Redmar-van-den-Berg merged 7 commits into from
Oct 23, 2025
Merged

update criteria for variant filtering and annotation #47

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c545f4c
update AML variant annotation criteria
AnnevdGrinten Oct 7, 2025
82a66a6
annotation of AML known pathogenic variants
AnnevdGrinten Oct 7, 2025
ca894b7
assume known_variants file has column names
AnnevdGrinten Oct 8, 2025
b989d1d
removed default so annotation col cannot be empty
AnnevdGrinten Oct 9, 2025
e8d0d2c
Merge branch 'main' of github.com:AnnevdGrinten/HAMLET
AnnevdGrinten Oct 23, 2025
e8e1a3e
small fixes in criteria after containment check
AnnevdGrinten Oct 23, 2025
8d042b9
Merge branch 'main' into main
Redmar-van-den-Berg Oct 23, 2025
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21 changes: 15 additions & 6 deletions utilities/deps/small-files/annotation_criteria.tsv
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Original file line number Diff line number Diff line change
@@ -1,13 +1,16 @@
gene_name transcript_id consequence start end frame annotation
NPM1 ENST00000296930.10 frameshift_variant 860 875 1 pathogenic
NPM1 ENST00000296930.10 discard
FLT3 ENST00000241453.12 missense_variant 2491 2526 likely pathogenic (FLT3-TKD)
FLT3 ENST00000241453.12 inframe_insertion 2491 2526 likely pathogenic (FLT3-TKD)
FLT3 ENST00000241453.12 inframe_deletion 2491 2526 likely pathogenic (FLT3-TKD)
FLT3 ENST00000241453.12 inframe_insertion 1705 1942 likely pathogenic (FLT3-ITD)
FLT3 ENST00000241453.12 discard
CEBPA ENST00000498907.3 inframe_deletion 814 1077 pathogenic (bZIP inframe)
CEBPA ENST00000498907.3 inframe_insertion 814 1077 pathogenic (bZIP inframe)
ASXL1 ENST00000375687.10 stop_gained 1720 4626 pathogenic
ASXL1 ENST00000375687.10 frameshift_variant 1720 4626 pathogenic
ASXL1 ENST00000375687.10 discard
BCOR ENST00000378444.9 frameshift_variant pathogenic
BCOR ENST00000378444.9 stop_gained pathogenic
BCOR ENST00000378444.9 stop_lost pathogenic
Expand All @@ -23,7 +26,7 @@ EZH2 ENST00000320356.7 inframe_insertion 1507 1851 possible pathogenic (CXC)
EZH2 ENST00000320356.7 missense_variant 1852 2253 possible pathogenic (SET)
EZH2 ENST00000320356.7 inframe_deletion 1852 2253 possible pathogenic (SET)
EZH2 ENST00000320356.7 inframe_insertion 1852 2253 possible pathogenic (SET)
EZH2 ENST00000320356.7 frameshift pathogenic
EZH2 ENST00000320356.7 frameshift_variant pathogenic
EZH2 ENST00000320356.7 stop_gained pathogenic
EZH2 ENST00000320356.7 stop_lost pathogenic
RUNX1 ENST00000675419.1 frameshift_variant pathogenic
Expand All @@ -45,6 +48,7 @@ SF3B1 ENST00000335508.11 stop_lost discard
SRSF2 ENST00000359995.10 missense_variant 283 284 pathogenic
SRSF2 ENST00000359995.10 inframe_insertion 283 284 pathogenic
SRSF2 ENST00000359995.10 inframe_deletion 283 284 pathogenic
SRSF2 ENST00000359995.10 discard
STAG2 ENST00000371145.8 frameshift_variant pathogenic
STAG2 ENST00000371145.8 start_lost pathogenic
STAG2 ENST00000371145.8 stop_gained pathogenic
Expand All @@ -57,6 +61,7 @@ U2AF1 ENST00000291552.9 inframe_deletion 100 105 possible pathogenic
U2AF1 ENST00000291552.9 missense_variant 466 477 possible pathogenic
U2AF1 ENST00000291552.9 inframe_insertion 466 477 possible pathogenic
U2AF1 ENST00000291552.9 inframe_deletion 466 477 possible pathogenic
U2AF1 ENST00000291552.9 discard
ZRSR2 ENST00000307771.8 frameshift_variant pathogenic
ZRSR2 ENST00000307771.8 start_lost pathogenic
ZRSR2 ENST00000307771.8 stop_gained pathogenic
Expand All @@ -68,7 +73,7 @@ TP53 ENST00000269305.9 start_lost pathogenic
TP53 ENST00000269305.9 stop_gained pathogenic
TP53 ENST00000269305.9 stop_lost pathogenic
TP53 ENST00000269305.9 missense_variant 742 744 pathogenic
TP53 ENST00000269305.9 missense possible pathogenic
TP53 ENST00000269305.9 missense_variant possible pathogenic
TP53 ENST00000269305.9 inframe_insertion possible pathogenic
TP53 ENST00000269305.9 inframe_deletion possible pathogenic
TP53g ENST00000455263.6 994-2 *2 possible pathogenic (alt exon 10 gamma)
Expand Down Expand Up @@ -99,20 +104,23 @@ KIT ENST00000288135.6 stop_lost discard
BRAF ENST00000646891.2 missense_variant 1768 1845 possible pathogenic
BRAF ENST00000646891.2 inframe_deletion 1768 1845 possible pathogenic
BRAF ENST00000646891.2 inframe_insertion 1768 1845 possible pathogenic
BRAF ENST00000646891.2 discard
CALR ENST00000316448.10 frameshift_variant 1090 1110 2 pathogenic (type-1 (like)
CALR ENST00000316448.10 frameshift_variant 1141 1251 2 pathogenic (type-2 (like)
CALR ENST00000316448.10 frameshift_variant 1111 1140 2 pathogenic (other)
CALR ENST00000316448.10 discard
CBL ENST00000264033.6 1096-2 1431+2 possible pathogenic (RING fingers)
CSF3R ENST00000373103.5 frameshift_variant 2041 2592 pathogenic (exon 17 truncating)
CSF3R ENST00000373103.5 stop_gained 2041 2592 pathogenic (exon 17 truncating)
CSF3R ENST00000373103.5 stop_lost 2041 2592 pathogenic (exon 17 truncating)
CSF3R ENST00000373103.5 missense_variant 1724 1864 possible pahtogenic (exon 14 activating)
CSF3R ENST00000373103.5 1724 1864 possible pathogenic
CSF3R ENST00000373103.5 discard
DNMT3A ENST00000321117.10 missense_variant 2644 2645 pathogenic
DNMT3A ENST00000321117.10 missense_variant possible pathogenic
DNMT3A ENST00000321117.10 inframe_deletion possible pathogenic
DNMT3A ENST00000321117.10 inframe_insertion possible pathogenic
DNMT3A ENST00000321117.10 frameshift possible pathogenic
DNMT3A ENST00000321117.10 frameshift_variant possible pathogenic
DNMT3A ENST00000321117.10 stop_gained possible pathogenic
DNMT3A ENST00000321117.10 stop_lost possible pathogenic
ETNK1 ENST00000671733.1 missense_variant 727 734 (only known pathogenic)
Expand Down Expand Up @@ -162,12 +170,13 @@ PTPN11 ENST00000351677.7 frameshift_variant discard
PTPN11 ENST00000351677.7 stop_gained discard
PTPN11 ENST00000351677.7 stop_lost discard
SETBP1 ENST00000649279.2 missense_variant 2548 2730 possible pathogenic
SETBP1 ENST00000649279.2 discard
TET2 ENST00000380013.9 frameshift_variant pathogenic
TET2 ENST00000380013.9 start_lost pathogenic
TET2 ENST00000380013.9 stop_gained pathogenic
TET2 ENST00000380013.9 start_lost pathogenic
TET2 ENST00000380013.9 missense_variant 3310 4443 possible pathogenic (Cat. Dom)
TET2 ENST00000380013.9 missense_variant 5527 6009 possible pathogenic (Cat. Dom)
TET2 ENST00000380013.9 missense_variant 3310 4443 possible pathogenic (cat. dom)
TET2 ENST00000380013.9 missense_variant 5527 6009 possible pathogenic (cat. dom)
UBA1 ENST00000335972.11 discard (only known pathogenic)
WT1 ENST00000452863.10 frameshift_variant 1114 1264 pathogenic
WT1 ENST00000452863.10 start_lost 1114 1264 pathogenic
Expand All @@ -180,4 +189,4 @@ GNB1 ENST00000378609.9 possible pathogenic
MYC ENST00000621592.8 175 240 possible pathogenic (MYC box 1)
NF1 ENST00000358273.9 possible pathogenic
PRPF8 ENST00000304992.11 possible pathogenic
RAD21 ENST00000297338.7 possible pathogenic
RAD21 ENST00000297338.7 possible pathogenic