Hi everyone,
I'm wondering if there's a consensus of what tools to use to visualise SNPs.
I have the data in the form of a SNP table across a number of individuals, and my wet-lab collaborators ask for a map of specific loci, ideally overlaid with genome annotation data.
The SNP table has been assembled from short-read sequencing data
(bowtie assembly -> samtools SNP calling -> samtools pileup per individual -> merger and some additional filtering).
The collaborators really just want to see the SNP positions (and what is there), not the underlying quality/coverage etc.
A quick search for available tools revealed:
- GeneSNP-VISTA (works with FASTA; I can indeed convert my SNP tables into FASTA per individual, but the application didn't start on my Mac)
- Tablet (looks cool, but is designed for quality/coverage formats such as SAM/BAM)
Would appreciate any recommendation, thanks!
I'm wondering if there's a consensus of what tools to use to visualise SNPs.
I have the data in the form of a SNP table across a number of individuals, and my wet-lab collaborators ask for a map of specific loci, ideally overlaid with genome annotation data.
The SNP table has been assembled from short-read sequencing data
(bowtie assembly -> samtools SNP calling -> samtools pileup per individual -> merger and some additional filtering).
The collaborators really just want to see the SNP positions (and what is there), not the underlying quality/coverage etc.
A quick search for available tools revealed:
- GeneSNP-VISTA (works with FASTA; I can indeed convert my SNP tables into FASTA per individual, but the application didn't start on my Mac)
- Tablet (looks cool, but is designed for quality/coverage formats such as SAM/BAM)
Would appreciate any recommendation, thanks!
Comment