How to extract protein coding sequence from fasta file?
Hi all
I used bcftools to generate a consensus sequence of a specific region of the chromosome from the hg38 and vcf file. So, I got the fasta file including genomic sequence of a specific region.
Finally, I want to get a protein coding sequence. Is there a way to extract the CDS from the fasta file?
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Do you already have an annotation for the gene you're interested in, or are you looking to predict this from the sequence?
I want to predict it from the sequence
sounds like a xy problem . Are you trying to predict the functional annotations of your variants : search this site for vep, snpeff, annovar, etc...