I am a student, and my report is causing me a lot of problems. I am a complete newbie, and I hope you could help me on my way.
I have problems with how I approach the following using Python:
I am looking at a cohort study investigating mutations in respectively lean and obese pigs compared to wildtype pig. I am supposed to determine which SNPs or mutations alter the amino acid sequence of the protein. It is a specific chromosome that is being investigated.
This are the files I have: I have a VCF file including information about the mutations. I have a CDS annotation file (a gtf file) with the protein coding region. I have a file where the VCF file has been intersected with the annotation file using bedtools, and then I have a fasta file with the genomic sequence of the chromosome investigated.
I am not sure how I approach this problem. I image that I have to do the following: Find the coding regions, so I have the coding regions of the wildtype. Then extract information from the VCF file to make a file with the sequence including the mutations. Then I can translate the wildtype sequence and mutation sequence and identify which mutations lead to a different amino acid sequence.
Does anyone have any tips or a guide for which python code I can use to find the coding regions, and possibly also extract the relevant information from the VCF file? I have used many days and hours without really going anywhere. Any help is therefore much appreciated!
Thank you!