Can we find SNP from fasta sequences ?

Question

[greyman]

I found the SNP from bam file and vcf workflow however I would like to try using FASTA for this process. Can we get Fasta format works?

[Joe]

I would like to compare the output of different files format

There is no real reason to do this. 'Proper' SNPs are called by mapping FASTQ files (which are just FASTA files with some quality information which gives you confidence in whether the SNP is real or not).

If you want to find variant sites between sets of sequences, you'd be looking at doing something like multiple sequence alignment instead.

[greyman]

As i wanted to extract the sequence region with SNP from exome data, is there anyway to do it from fastq? Last time when i use fasta i extract the gene sequence from whole genome data that has been split into gene data

[Joe]

Don't bother using the FASTA/FASTQ data once you've done the mapping. If you have your BAM/SAM file, you can extract subregions directly from those I believe, so you can capture your specific site of interest.

[WouterDeCoster]

This doesn't sound like a good idea. Using fastq to reference alignment and a well-characterized variant caller is probably going to be more reliable than rolling your own solution based on fasta records. Just don't :)

[ATpoint]

You might want to read and apply this tutorial ;-D

[Bastien Hervé]

Sorry, but this explanation is really messy. What do you want to do biologicaly. Note that you can't call SNPs on fasta files, you need to have the associated quality

Answer 1

[Emily]

1. Align FASTQ to genome reference to get BAM files.
2. Perform SNP calling on BAM files.