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LOVDnl / LOVD3

LOVD3 development repository
http://www.LOVD.nl
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LOVD2 converter: Warning: linked "Variant/DbSNP" to non-existing column "VariantOnTranscript/DbSNP" in output section "Variants_On_Transcripts". #437

Closed ifokkema closed 4 years ago

ifokkema commented 4 years ago

Reported by Wei Kheng Teh; While converting an LOVD2 file to the LOVD3 format:

Warning: linked "Variant/DbSNP" to non-existing column "VariantOnTranscript/DbSNP" in output section "Variants_On_Transcripts".

This should be mapped to VariantOnGenome/dbSNP.

Wkt8 commented 4 years ago

LOVD-version 2000-360 ### Variants/Patients ### Do not remove this line, unless importing in versions before 2.0-04

"{{ Variant/Exon }}" "{{ Variant/DNA }}" "{{ Variant/DbSNP }}" "{{ Variant/Type }}" "{{ Variant/Consequence/Predicted }}" "{{ Variant/Protein }}" "{{ Variant/RNA }}" "{{ Variant/Restriction_site }}" "{{ Variant/Frequency }}" "{{ Variant/DBID }}" "{{ Patient/Patient_ID }}" "{{ Patient/Phenotype/Disease }}" "{{ Patient/Reference }}" "{{ Patient/Detection/Template }}" "{{ Patient/Detection/Technique }}" "{{ Patient/Remarks }}" "{{ Patient/Remarks_Non_Public }}" "{{ Patient/Origin/Ethnic }}" "{{ IDvariantid }}" "{{ IDpatientid }}" "{{ IDallele }}" "{{ IDpathogenic }}" "{{ IDstatus }}" "{{ IDsort }}" "{{ IDsubmitterid }}" "{{ ID_variant_createdby }}" "{{ variant_createddate }}" "{{ ID_variant_editedby }}" "{{ variant_editeddate }}" "{{ ID_patient_createdby }}" "{{ patient_createddate }}" "{{ ID_patient_editedby }}" "{{ patient_editeddate }}" "01" "c.2T>C" "" "substitution" "initiating methionine" "p.?" "" "" "" "ADAMTS2_00008" "AN_001995" "Dermatosparaxis EDS" "{PMID26765342:Van Damme et al., 2016}" "DNA" "PCR;SEQ" "" "" "" "0000010" "0001462" "11" "99" "9" "0001_0000002_0000000" "00004" "0" "2015-07-31 10:21:53" "1" "2015-11-16 14:52:31" "0" "2015-07-31 10:21:53" "1" "2016-01-18 16:34:30" "01" "c.102_123dup" "" "duplication" "frameshift" "p.Ala42Argfs*31" "" "" "" "ADAMTS2_00018" " " "" "{PMID31939527:Bo et al., 2020}" "DNA" "WES" "The patient was diagnosed with situs inversus totalis, and idiopathic thrombocytopenia purpura. The variant was described in the paper as an insertion at c.123_124, but is in fact a duplication of c.102_123. It was detected via exome sequencing, and thus the authors were uncertain if the patient had compound heterogeneity for another variant in ADAMTS2. " "" "" "0000020" "0001841" "0" "11" "9" "0001_0000102_0000000_0000123_0000000" "00000" "9" "2020-05-11 16:38:18" "9" "2020-05-11 16:38:24" "9" "2020-05-11 16:38:18" "9" "2020-05-11 16:39:24"

Wkt8 commented 4 years ago

LOVD-version 2000-360 ### Variants/Patients ### Do not remove this line, unless importing in versions before 2.0-04

"{{ Variant/Exon }}" "{{ Variant/DNA }}" "{{ Variant/DbSNP }}" "{{ Variant/Type }}" "{{ Variant/Consequence/Predicted }}" "{{ Variant/Protein }}" "{{ Variant/RNA }}" "{{ Variant/Restriction_site }}" "{{ Variant/Frequency }}" "{{ Variant/DBID }}" "{{ Patient/Patient_ID }}" "{{ Patient/Phenotype/Disease }}" "{{ Patient/Reference }}" "{{ Patient/Detection/Template }}" "{{ Patient/Detection/Technique }}" "{{ Patient/Remarks }}" "{{ Patient/Remarks_Non_Public }}" "{{ Patient/Origin/Ethnic }}" "{{ IDvariantid }}" "{{ IDpatientid }}" "{{ IDallele }}" "{{ IDpathogenic }}" "{{ IDstatus }}" "{{ IDsort }}" "{{ IDsubmitterid }}" "{{ ID_variant_createdby }}" "{{ variant_createddate }}" "{{ ID_variant_editedby }}" "{{ variant_editeddate }}" "{{ ID_patient_createdby }}" "{{ patient_createddate }}" "{{ ID_patient_editedby }}" "{{ patient_editeddate }}" "01" "c.2T>C" "" "substitution" "initiating methionine" "p.?" "" "" "" "ADAMTS2_00008" "AN_001995" "Dermatosparaxis EDS" "{PMID26765342:Van Damme et al., 2016}" "DNA" "PCR;SEQ" "" "" "" "0000010" "0001462" "11" "99" "9" "0001_0000002_0000000" "00004" "0" "2015-07-31 10:21:53" "1" "2015-11-16 14:52:31" "0" "2015-07-31 10:21:53" "1" "2016-01-18 16:34:30" "01" "c.102_123dup" "" "duplication" "frameshift" "p.Ala42Argfs*31" "" "" "" "ADAMTS2_00018" "-" "" "{PMID31939527:Bo et al., 2020}" "DNA" "WES" "The patient was diagnosed with situs inversus totalis, and idiopathic thrombocytopenia purpura. The variant was described in the paper as an insertion at c.123_124, but is in fact a duplication of c.102_123. It was detected via exome sequencing, and thus the authors were uncertain if the patient had compound heterogeneity for another variant in ADAMTS2. " "" "" "0000020" "0001841" "0" "11" "9" "0001_0000102_0000000_0000123_0000000" "00000" "9" "2020-05-11 16:38:18" "9" "2020-05-11 16:38:24" "9" "2020-05-11 16:38:18" "9" "2020-05-11 16:39:24" "02" "c.220G>A" "{dbSNPrs2271211}" "substitution" "missense" "p.Val74Met" "" "" "" "ADAMTS2_00014" "-" "DAD" "{PMID32095376:Chen et al., 2020}" "DNA" "WES;WGS" "This deleterious SNP is highly associated with intracranial aneurysm. " "" "Han Chinese" "0000016" "0001837" "0" "11" "9" "0002_0000220_0000000" "00000" "9" "2020-05-05 15:25:45" "9" "2020-05-05 15:30:48" "9" "2020-05-05 15:25:45" "9" "2020-05-05 15:26:02"