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Description
Recently, I encountered a complex variant with an IGV image of
Simply put, this mutation is
GGAATTAAGAGAAG
G---------GAAC
I called it using mutet2, and ultimately it was represented as
#CHROM POS ID REF ALT QUAL FILTER INFO
7 55242465 . GGAATTAAGA G . . .
7 55242478 . G C . . .
This seems to follow the left alignment rule
But according to the 3'rule of hgvs
(I confirmed the direction of my focus on transcript NM_005228)
this mutation is
GGAATTAAGAGAAG
GGAA---------C
#CHROM POS ID REF ALT QUAL FILTER INFO
7 55242469 . TTAAGAGAAG C . . .
I also annotated the final results using VEP. Obviously, VEP does not merge p.hgvs variants.
7 55242465 . GGAATTAAGA G . . CSQ=-|inframe_deletion|MODERATE|EGFR|1956|Transcript|NM_001346897.2|protein_coding|18/26||NM_001346897.2:c.2104_2112del|NP_001333826.1:p.Leu702_Glu704del|2362-2370/3848|2101-2109/3276|701-703/1091|ELR/-|GAATTAAGA/-|rs121913436|1||1|||deletion|EntrezGene|||||NP_001333826.1||||||||||||3||||||||||||||||||drug_response||1||||||,-|inframe_deletion|MODERATE|EGFR|1956|Transcript|NM_001346898.2|protein_coding|19/27||NM_001346898.2:c.2239_2247del|NP_001333827.1:p.Leu747_Glu749del|2497-2505/3983|2236-2244/3411|746-748/1136|ELR/-|GAATTAAGA/-|rs121913436|1||1|||deletion|EntrezGene|||||NP_001333827.1||||||||||||3||||||||||||||||||drug_response||1||||||,-|inframe_deletion|MODERATE|EGFR|1956|Transcript|NM_001346899.2|protein_coding|18/27||NM_001346899.2:c.2104_2112del|NP_001333828.1:p.Leu702_Glu704del|2362-2370/9770|2101-2109/3498|701-703/1165|ELR/-|GAATTAAGA/-|rs121913436|1||1|||deletion|EntrezGene|||||NP_001333828.1||||||||||||3||||||||||||||||||drug_response||1||||||,-|inframe_deletion|MODERATE|EGFR|1956|Transcript|NM_001346900.2|protein_coding|19/28||NM_001346900.2:c.2080_2088del|NP_001333829.1:p.Leu694_Glu696del|2268-2276/9676|2077-2085/3474|693-695/1157|ELR/-|GAATTAAGA/-|rs121913436|1||1|||deletion|EntrezGene|||||NP_001333829.1||||||||||||3||||||||||||||||||drug_response||1||||||,-|inframe_deletion|MODERATE|EGFR|1956|Transcript|NM_001346941.2|protein_coding|13/22||NM_001346941.2:c.1438_1446del|NP_001333870.1:p.Leu480_Glu482del|1696-1704/9104|1435-1443/2832|479-481/943|ELR/-|GAATTAAGA/-|rs121913436|1||1|||deletion|EntrezGene|||||NP_001333870.1||||||||||||3||||||||||||||||||drug_response||1||||||,-|inframe_deletion|MODERATE|EGFR|1956|Transcript|NM_005228.5|protein_coding|19/28||NM_005228.5:c.2239_2247del|NP_005219.2:p.Leu747_Glu749del|2497-2505/9905|2236-2244/3633|746-748/1210|ELR/-|GAATTAAGA/-|rs121913436|1||1||1|deletion|EntrezGene||YES|||NP_005219.2||||||||||||3||||||||||||||||||drug_response||1||||||,-|downstream_gene_variant|MODIFIER|EGFR|1956|Transcript|NM_201284.2|protein_coding||||||||||rs121913436|1|3736|1|||deletion|EntrezGene|||||NP_958441.1||||||||||||||||||||||||||||||drug_response||1||||||,-|downstream_gene_variant|MODIFIER|EGFR-AS1|100507500|Transcript|NR_047551.1|lncRNA||||||||||rs121913436|1|4969|-1|||deletion|EntrezGene||YES|||||||||||||||||||||||||||||||||drug_response||1||||||
7 55242478 . G C . . CSQ=C|missense_variant|MODERATE|EGFR|1956|Transcript|NM_001346897.2|protein_coding|18/26||NM_001346897.2:c.2113G>C|NP_001333826.1:p.Ala705Pro|2374/3848|2113/3276|705/1091|A/P|Gca/Cca|rs121913229&COSV51830861|1||1|||SNV|EntrezGene|||||NP_001333826.1|||||||||tolerated(0.24)|probably_damaging(0.942)||||||||||||||||||||likely_pathogenic&uncertain_significance|0&1|1&1|25157968&15737014&22622260|||||,C|missense_variant|MODERATE|EGFR|1956|Transcript|NM_001346898.2|protein_coding|19/27||NM_001346898.2:c.2248G>C|NP_001333827.1:p.Ala750Pro|2509/3983|2248/3411|750/1136|A/P|Gca/Cca|rs121913229&COSV51830861|1||1|||SNV|EntrezGene|||||NP_001333827.1|||||||||tolerated(0.26)|probably_damaging(0.995)||||||||||||||||||||likely_pathogenic&uncertain_significance|0&1|1&1|25157968&15737014&22622260|||||,C|missense_variant|MODERATE|EGFR|1956|Transcript|NM_001346899.2|protein_coding|18/27||NM_001346899.2:c.2113G>C|NP_001333828.1:p.Ala705Pro|2374/9770|2113/3498|705/1165|A/P|Gca/Cca|rs121913229&COSV51830861|1||1|||SNV|EntrezGene|||||NP_001333828.1|||||||||tolerated(0.19)|probably_damaging(0.998)||||||||||||||||||||likely_pathogenic&uncertain_significance|0&1|1&1|25157968&15737014&22622260|||||,C|missense_variant|MODERATE|EGFR|1956|Transcript|NM_001346900.2|protein_coding|19/28||NM_001346900.2:c.2089G>C|NP_001333829.1:p.Ala697Pro|2280/9676|2089/3474|697/1157|A/P|Gca/Cca|rs121913229&COSV51830861|1||1|||SNV|EntrezGene|||||NP_001333829.1|||||||||tolerated(0.21)|probably_damaging(0.942)||||||||||||||||||||likely_pathogenic&uncertain_significance|0&1|1&1|25157968&15737014&22622260|||||,C|missense_variant|MODERATE|EGFR|1956|Transcript|NM_001346941.2|protein_coding|13/22||NM_001346941.2:c.1447G>C|NP_001333870.1:p.Ala483Pro|1708/9104|1447/2832|483/943|A/P|Gca/Cca|rs121913229&COSV51830861|1||1|||SNV|EntrezGene|||||NP_001333870.1|||||||||tolerated(0.2)|probably_damaging(0.986)||||||||||||||||||||likely_pathogenic&uncertain_significance|0&1|1&1|25157968&15737014&22622260|||||,C|missense_variant|MODERATE|EGFR|1956|Transcript|NM_005228.5|protein_coding|19/28||NM_005228.5:c.2248G>C|NP_005219.2:p.Ala750Pro|2509/9905|2248/3633|750/1210|A/P|Gca/Cca|rs121913229&COSV51830861|1||1||1|SNV|EntrezGene||YES|||NP_005219.2|||||||||tolerated(0.18)|probably_damaging(0.942)||||||||||||||||||||likely_pathogenic&uncertain_significance|0&1|1&1|25157968&15737014&22622260|||||,C|downstream_gene_variant|MODIFIER|EGFR|1956|Transcript|NM_201284.2|protein_coding||||||||||rs121913229&COSV51830861|1|3748|1|||SNV|EntrezGene|||||NP_958441.1||||||||||||||||||||||||||||||likely_pathogenic&uncertain_significance|0&1|1&1|25157968&15737014&22622260|||||,C|downstream_gene_variant|MODIFIER|EGFR-AS1|100507500|Transcript|NR_047551.1|lncRNA||||||||||rs121913229&COSV51830861|1|4965|-1|||SNV|EntrezGene||YES|||||||||||||||||||||||||||||||||likely_pathogenic&uncertain_significance|0&1|1&1|25157968&15737014&22622260|||||
7 55242469 . TTAAGAGAAG C . . CSQ=C|protein_altering_variant|MODERATE|EGFR|1956|Transcript|NM_001346897.2|protein_coding|18/26||NM_001346897.2:c.2104_2113delinsC|NP_001333826.1:p.Leu702_Ala705delinsPro|2365-2374/3848|2104-2113/3276|702-705/1091|LREA/P|TTAAGAGAAGca/Cca|rs727504278&COSV51765099|1||1|||indel|EntrezGene|||||NP_001333826.1||||||||||||||||||||||||||||||drug_response|0&1|1&1|24033266|||||,C|protein_altering_variant|MODERATE|EGFR|1956|Transcript|NM_001346898.2|protein_coding|19/27||NM_001346898.2:c.2239_2248delinsC|NP_001333827.1:p.Leu747_Ala750delinsPro|2500-2509/3983|2239-2248/3411|747-750/1136|LREA/P|TTAAGAGAAGca/Cca|rs727504278&COSV51765099|1||1|||indel|EntrezGene|||||NP_001333827.1||||||||||||||||||||||||||||||drug_response|0&1|1&1|24033266|||||,C|protein_altering_variant|MODERATE|EGFR|1956|Transcript|NM_001346899.2|protein_coding|18/27||NM_001346899.2:c.2104_2113delinsC|NP_001333828.1:p.Leu702_Ala705delinsPro|2365-2374/9770|2104-2113/3498|702-705/1165|LREA/P|TTAAGAGAAGca/Cca|rs727504278&COSV51765099|1||1|||indel|EntrezGene|||||NP_001333828.1||||||||||||||||||||||||||||||drug_response|0&1|1&1|24033266|||||,C|protein_altering_variant|MODERATE|EGFR|1956|Transcript|NM_001346900.2|protein_coding|19/28||NM_001346900.2:c.2080_2089delinsC|NP_001333829.1:p.Leu694_Ala697delinsPro|2271-2280/9676|2080-2089/3474|694-697/1157|LREA/P|TTAAGAGAAGca/Cca|rs727504278&COSV51765099|1||1|||indel|EntrezGene|||||NP_001333829.1||||||||||||||||||||||||||||||drug_response|0&1|1&1|24033266|||||,C|protein_altering_variant|MODERATE|EGFR|1956|Transcript|NM_001346941.2|protein_coding|13/22||NM_001346941.2:c.1438_1447delinsC|NP_001333870.1:p.Leu480_Ala483delinsPro|1699-1708/9104|1438-1447/2832|480-483/943|LREA/P|TTAAGAGAAGca/Cca|rs727504278&COSV51765099|1||1|||indel|EntrezGene|||||NP_001333870.1||||||||||||||||||||||||||||||drug_response|0&1|1&1|24033266|||||,C|protein_altering_variant|MODERATE|EGFR|1956|Transcript|NM_005228.5|protein_coding|19/28||NM_005228.5:c.2239_2248delinsC|NP_005219.2:p.Leu747_Ala750delinsPro|2500-2509/9905|2239-2248/3633|747-750/1210|LREA/P|TTAAGAGAAGca/Cca|rs727504278&COSV51765099|1||1||1|indel|EntrezGene||YES|||NP_005219.2||||||||||||||||||||||||||||||drug_response|0&1|1&1|24033266|||||,C|downstream_gene_variant|MODIFIER|EGFR|1956|Transcript|NM_201284.2|protein_coding||||||||||rs727504278&COSV51765099|1|3739|1|||indel|EntrezGene|||||NP_958441.1||||||||||||||||||||||||||||||drug_response|0&1|1&1|24033266|||||,C|downstream_gene_variant|MODIFIER|EGFR-AS1|100507500|Transcript|NR_047551.1|lncRNA||||||||||rs727504278&COSV51765099|1|4965|-1|||indel|EntrezGene||YES|||||||||||||||||||||||||||||||||drug_response|0&1|1&1|24033266|||||
I am looking for tools to adjust the location of del occurrence based on the direction of the transcript of interest to meet the final HGVS requirements.
It seems that bcftool cannot achieve this either,
Can corresponding functions be added? Thank you for any suggestions