codon changes finding in gene

Question

[fatimarasool135]

Hi, I have to find the codon changes in genes. how can i find ? is there any script or tool for resolving this problem ? I have the coordinate of allele like > 1A 124189778 124189779 and corresponding gene in which > GA changes occurred. the numbers of genes are in hundreds and finding codon chages one by one by ENSEMBL database is very time taking.

chr coordinate  coordinate  base_change  gene-name    Amino_acid_change

1A  124189778   124189779   GA          gene1                 ?
1A  124189787   124189788   GA          gene2                 ?
1A  124189792   124189793   GA          gene3                 ?

[Pierre Lindenbaum]

this question has been asked many times on this site. Please search for "VEP" , "SnpEff", etc...

[fatimarasool135]

VEP and SnpEff take the input file as VCF file. I have file in partially bed format contain chr_name, coordinate , allel change..these 3 information only. so this file is not according to input file format of VEP and SnpEff.

[Pierre Lindenbaum]

you just have to reformat your input.

Molecular biology is 90% moving small liquids from one tube to another. Computational biology is 90% file manipulation.

— Stephen Williams (@SvenAT) August 2, 2016

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[fatimarasool135]

Dear Pierre Lindenbaum, now i have change the format of file according to VEP tool. this tool can take the input file as mention in this link [https://plants.ensembl.org/info/docs/tools/vep/vep_formats.html#default]

here is my file

1A 124189766 124189766 GA +

1A 124189779 124189779 GA +

1A 124189788 124189788 GA +

1A 124189793 124189793 GA +

this file format is Default VEP input, but still i got the error that input file format is not correct. i have use the online VEP.