Snp Analysis In 454 Sequences

Question

[Emmecola]

Hi!

I need a software to find SNPs in sequences obtained with 454 sequencing (RNA-seq). Which software would you suggest?

Thank you very much

[Eric Normandeau]

Hi emmecola. Please take time to detail your question in order to get more meaningfull answers. For example: What format are the data in? Have you already proceeded through the assembly step? What is your system of interest? (could have an impact on how likely paralogous sequences are, for example). Do not hesitate to give more contextual information. Cheers!

Answer 1

[Rm]

Very Nice and simple description of protocol(s) using illumina/454 reads for SNP detection using BWA, samtools, GATK and IGV

RNA-Seq Blog

Answer 2

[Erik Garrison]

For long reads such as 454, Mosaik performs quite well, particularly if you are interested in insertions and deletions--- although pyrosequencing tends to produce a lot of homopolymer runs in the data which can frustrate indel detection.

FreeBayes, which operates on BAM files as produced by most contemporary short-read aligners, can be used to detect SNPs and short (less than read-length) insertions and deletions. (I am the author.)

If you want to obtain the highest-possible quality dataset, I recommend using multiple approaches to obtain your list of variations, and then intersecting this set between different approaches. This can help you to remove variants which are artifacts of a specific computation methods.

Alternatively, you can take a union of different approaches to find the variants which specific algorithms miss, and then filter the resulting dataset using reported variant quality metrics (as found in the VCF files which the variant detectors output).