Hi!,
I am trying to figure out the connectivity between subpopulations of a parrotfish species along the coast of western Africa by analyzing the differences of neutral mutations in SNPs in the COI region between the subpopulations and trying to correlate these to the coastal currents.
I have done sanger sequencing for around a hundred samples, I have bi-directionally sequenced these and then aligned the pairs to get one consensus sequence per sample. However, I have now gotten stuck since most analyzing programs and packages use the newer VCF format rather than the FASTA format that I got the results in.
Is there a way to convert the FASTA sequences to VCF?
There are several sequences of the same gene in Genbank that I could use as a reference if needed.
Thankfull for any help or input!
Making the wrong question.
You need to map/align the sanger reads to a reference sequence (COI) to identify polymorphisms. The mapping step should generate a SAM file that needs to be converted to a BAM and then used with a software such as GATK/SAMtools/freebayes to generate the VCF file.
It should be somehow straightforward.
Hi Erik,
Thank you for your answer!
I'm sort of a beginner with bioinformatics as you probably understand, but I was thinking to use a reference sequence from genbank to do the alignments. Should I align/map the consensus of the reads from the two primers of each sample? and do you recommend any good tool to do that and to generate the SAM file?
Thank you so much for the help!
Hi Erik Diaz ,
Thank you for your answer!
I'm sort of a beginner with bioinformatics as you probably understand, but I was thinking to use a reference sequence from genbank to do the alignments. Should I align/map the consensus of the reads from the two primers of each sample? and do you recommend any good tool to do that and to generate the SAM file?
Thank you so much for the help!
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