This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Extract Di-nucleotide/Tri-Nucleotide substitution frequencies from MSA/VCF file

Hello,

I have 3 samples of Viral sequences for three different time points. Each sample has 100+ Near-full length HIV sequences (~8000 bp). I have remove the sequences with deletions and have only the intact viral sequences.

I would like to get the substitution frequency of dinucleotides & trinucleotides for each sample. I have previously found the SNP substitution frequency using VCFstats package (https://pwwang.github.io/vcfstats/).

Are there any available algorithms to extract this information from either a Multi-Seq Alignment or VCF file?

Thanks, Sara

msa substitution vcfstats evolution vcf
• 817 views • link
updated by Pierre Lindenbaum Pierre Lindenbaum • written by Saran • Saran

Don't forget to follow up on your threads. If an answer was helpful, you should upvote it; if the answer resolved your question, you should mark it as accepted. You can accept more than one answer if they all work. If an answer was not really helpful or did not work, provide detailed feedback so others know not to use that answer.

Upvote|Bookmark|Accept

• 0 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

0 answers

No answers yet.

Log in to answer this question.

More posts like this