Whole Genome Seq Analysis Software for Identifying Specific Gene Variants

Question

[dk0319]

What are some of the popular free software tools for analyzing whole genome sequencing data? I am particularly interested in analyzing the sequences that map to a particular gene region in order to confirm predicted variation in the sequence. So if anyone as any recommendations, I am very interested to hear them, as I have never done WGS analysis before, only RNA-seq.

[Pierre Lindenbaum]

what did you find so far ?

[dk0319]

I have used commercial like CLC and snapgene in the past. As for free there is star, bowtie and Rsubread. But, I use those for RNA-seq not WGS. And none of them provide a visual map, apart from the commercial, at least as far as I know.

Answer 1

[swbarnes2]

If all you want to do is look at one gene, I'd eyeball it in IGV. Any aligner that works with RNASeq will work fine for DNA, and the indexed bam can be read into IGV.

https://software.broadinstitute.org/software/igv/download