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I have a list of chromosomes, positions, gene ids, and transcript ids (from a gencode GTF file) - how can I get their corresponding REF and ALT values?

I have the latest Gencode GTF file filtered down to just the rows with exon information, that looks like the following:

chr1    HAVANA  exon    65419   65433       +       gene_id "ENSG00000186092"; transcript_id "ENST00000641515"; gene_type "protein_coding"; gene_name "OR4F5"; transcript_type "protein_coding"; transcript_name "OR4F5-202"; exon_number 1; exon_id "ENSE00003812156"; level 2; protein_id "ENSP00000493376"; tag "RNA_Seq_supported_partial"; tag "basic"; havana_gene "OTTHUMG00000001094"; havana_transcript "OTTHUMT00000003223";
chr1    HAVANA  exon    65520   65573       +       gene_id "ENSG00000186092"; transcript_id "ENST00000641515"; gene_type "protein_coding"; gene_name "OR4F5"; transcript_type "protein_coding"; transcript_name "OR4F5-202"; exon_number 2; exon_id "ENSE00003813641"; level 2; protein_id "ENSP00000493376"; tag "RNA_Seq_supported_partial"; tag "basic"; havana_gene "OTTHUMG00000001094"; havana_transcript "OTTHUMT00000003223";
chr1    HAVANA  exon    69037   71585       +       gene_id "ENSG00000186092"; transcript_id "ENST00000641515"; gene_type "protein_coding"; gene_name "OR4F5"; transcript_type "protein_coding"; transcript_name "OR4F5-202"; exon_number 3; exon_id "ENSE00003813949"; level 2; protein_id "ENSP00000493376"; tag "RNA_Seq_supported_partial"; tag "basic"; havana_gene "OTTHUMG00000001094"; havana_transcript "OTTHUMT00000003223";

I'm trying to turn this file into one that will have the columns Chromosome, Position, Ref, Alt, Gene, Transcript - how can I get the corresponding Ref and Alt values based on the gencode input file above?

genome gencode
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written by claudiadast • claudiadast

Hello claudiadast ,

could you please explain why you like to do this? GTF have no information about REF and ALT. It just describes a certain feature (in your case "exon") in a given region.

fin swimmer

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written by finswimmer finswimmer

Hi, yes I know, but I thought the GTF still gives me sufficient information (Gene, chromosome, position) to look up REF and ALT online.

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written by claudiadast • claudiadast

Hello again,

it is still not clear what you are trying to do and why. Please descibe this to get proper help.

Thanks!

fin swimmer

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written by finswimmer finswimmer

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