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!
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!
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