SNP Analysis Tools for SOLiD

[chrnlng]

Hi all,

I've just completed sequencing and aligning data from 200 patients and was wondering if what would be the best SNP calling tools to use for this data? Currently I'm using CRISP and Syzygy as those are what my colleagues are using but, unless I'm mistaken, these were designed to call SNPs from data arising from Illumina reads and don't use the colour space data from the SOLiD reads. I have also been recommended GATK but as far as I am aware that is only for single genome SNP calling.
So, if anyone knows of a good SNP calling tool for SOLiD I would be really grateful for any help! If it helps I've divided my patients up into 4 pools of 50 patients each.

Thanks!

[snetmcom]

dibayes was their internal recommended caller i believe. i'm not sure if it's still hosted.

[RFo]

yeah, i normally use dibayes, it's part of the lifescope package (http://www.lifetechnologies.com/glob...-software.html).
You can also use other tools, such as samtools mpileup (http://samtools.sourceforge.net/mpileup.shtml), but use lifescope for mapping and carry on using its output (bam-files). The bam files are in basespace.

[lethalfang]

Hi all,

I've just completed sequencing and aligning data from 200 patients and was wondering if what would be the best SNP calling tools to use for this data? Currently I'm using CRISP and Syzygy as those are what my colleagues are using but, unless I'm mistaken, these were designed to call SNPs from data arising from Illumina reads and don't use the colour space data from the SOLiD reads. I have also been recommended GATK but as far as I am aware that is only for single genome SNP calling.
So, if anyone knows of a good SNP calling tool for SOLiD I would be really grateful for any help! If it helps I've divided my patients up into 4 pools of 50 patients each.

Thanks!

What did you use to align the data?
The aligner that SOLiD typically comes with does SNP calling as well.

http://solid.community.appliedbiosystems.com/community/about_solid/blog/2012/04/15/lifescope-genomic-analysis-software-251

[Zaag]

You can use GATK for this.