We have sequenced a few inbred lines (whole genome sequencing) and identified thousands of SNPs. I would like to select a few hundred informative SNPs based on PIC among our inbreds for SNP genotyping. I appreciate if anyone could suggest tools or software to shortlist SNPs.
Thanks in advance
Dear Raghavendra
As I see from your affiliation, yours is a seed company. The best way you could do is NOT just the PIC but also look into some classes of SNPs with good gene diversity scores. The gramene has a database for that.
The best scores per probability value can be checked from dbSNP, if your organism is listed in GenBank
Hope this helps
Prash
First, to make sure what you found are SNPs and not, for instance, diffrences between similar repeating sequences in the genome, you should select SNPs that have a cover within the 0.25 and 0.75 quantiles of the sequencing cover distribution.
I don't know what is your organism, or how many inbred lines you've sequenced. If there is a draft genome for your organism, then of course you should try and take SNPs that are spread more or less equally along the genome.
I guess since it's inbred lines, that they are homozygous for most of the SNPs. If you have SNPs that are heterozygous in some of the lines it might be a good idea to take those, but DON'T take SNPs that are heterozygous in all the lines.
Try to take groups of SNPs that differentiate between different groups of lines. In fact, try to take at least few SNPs that differentiate between each pair of lines.
Good luck,
Mor
You have to have reference sequence and library of geographically separated isolates.(10-100). Compare all sequences together and exclude one time SNP. All SNPs found in multiple genomes can be analyzed according to geographical appearance or pathogenicity or else to form genotyping groups with identical genotypes,
Look at my paper
Loparev VN, Gonzalez A, Deleon-Carnes M, Tipples G, Fickenscher H, Torfason EG, Schmid DS.Global identification of three major genotypes of varicella-zoster virus: longitudinal clustering and strategies for genotyping.
J Virol. 2004 Aug;78(15):8349-58.
Loparev VN, Rubtcova EN, Bostik V, Tzaneva V, Sauerbrei A, Robo A, Sattler-Dornbacher E, Hanovcova I, Stepanova V, Splino M, Eremin V, Koskiniemi M, Vankova OE, Schmid DS.Distribution of varicella-zoster virus (VZV) wild-type genotypes in northern and southern Europe: evidence for high conservation of circulating genotypes.
Virology. 2009 Jan 20;383(2):216-25. doi: 10.1016/j.virol.2008.10.026. Epub 2008 Nov 20.
We did VZV genotyping wit 4-6 SNP
Thank you all for your responses. I wonder if there are any software/program to extract such SNPs. I have well built reference genome, BAM files of all inbreds and also SNPs identified for each genome with reference to reference assembly. I need shortlist SNPs that are polymorphic among inbreds and are uniformly distributed across the genome
For selecting informative SNPs, I use sample sub-sampling to generate SNP frequency distributions for the population, then pick out the SNPs that are most differentiated between two populations. If you're looking for within-population diversity, then you can pick the SNPs that have the greatest spread of frequencies among different sub-samples. I don't have any specific software to do this, but my method is outlined in Chapter 5 of my thesis, where I use a subsampling method to pick informative SNPs for T1D risk prediction:
https://www.researchgate.net/publication/257938344_Genomic_analysis_of_Human_Population_Structure
Thesis Genomic analysis of Human Population Structure
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