Help with SNP calling

[Barney Wharam]

Dear All,

In reference to the NGS workshop in Sheffield that I attended I've been trying to use Victor's RAD mapping practical to help me with my own SNP calling. I first wanted to ask whether I am approaching this in the correct manner.

I have 20 strains of C. elegans which have all been sequenced be genepool in edinburgh. The files when given to me were in a <strain>_3_run_elemt_sorted_realigned.sorted.bam format which I presume corresponds roughly with the sorted.bam files on slide 54 of Victors practical RAD_mapping.ppt

I have produced a .vcf with a long list of SNPs for each strain.

What can I do to then identify non-synonymous SNPs in specific loci - baring in mind that C. elegans has a well annotated genome.

Genome viewers such as IGV can open sorted.bam files (http://www.broadinstitute.org/igv/) and show very clearly SNP calling including phred scores and other useful information, but it is quite painstaking to do this SNP by SNP on what is essentially a very graphical format. 

I thought that the best way to do this would be to look at my .vcf files in IGV or on Galaxy, but my .vcf files are around 10GB so are way over the limit for galaxy upload or viewing in IGV. 

Is the fact that my .vcf is so large alarming? and if so is this due to insufficient filtering? baring in mind that it is whole genome variant calling.

Any help would be much appreciated, 

Best wishes

Barney

[Victor Soria-Carrasco]

Hi Barney,

I am sorry I don't have too much time to look into this this week, but I
have found this thread: http://seqanswers.com/forums/showthread.php?t=20061

In particular, the scripts available here:
http://users.ugent.be/~slvbelle/NGS/ seem to do exactly what you want.

Cheers,

Victor

__
Victor Soria-Carrasco
Post-doctoral Research Associate
Nosil Lab of Evolutionary Biology
Department of Animal and Plant Sciences
University of Sheffield
Western Bank
Sheffield S10 2TN
United Kingdom

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