Read stats on SNP after GBSHapMapFiltersPlugin

[Sheina Sim]

Is there any way to generate a VCF file after the SNPs are merged and filtered?

I would like to get some basic stats on the read depth of each locus and per individual for only the SNPs we get after running MergeTagsByTaxaFilesPlugin and GBSHapMapFiltersPlugin.  

Thanks!

[Jeff Glaubitz]

Open the hmp format genotype file in the Tassel 5 GUI (Data|Load) and then export it as VCF (Data|Export).

 

Or use the Tassel 5 command line:

/path/to/tassel5-standalone/run_pipeline.pl -Xmx4g -fork1 -h myGenos.hmp.txt.gz -export myGenos.vcf -exportType VCF -runfork1

 

Substituting the actual name of your file for “myGenos”.

 

--

Jeff Glaubitz

Project Manager

Biology of Rare Alleles in Maize and its Wild Relatives

National Science Foundation award IOS-1238014

http://www.panzea.org

Institute for Genomic Diversity

Cornell University

175 Biotechnology Bldg

Ithaca, NY 14853

Phone: 607-255-1386

jcg...@cornell.edu

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[Sheina Sim]

Hi Jeff,

Thanks for your reply!  I have used one of the Tassel modules before to change my .hmp file into a .vcf file, and though some things changed (the file extension and some comments appeared), the file did not actually have the sort of read information I was looking for since .hmp files do not have that sort of read information.  Is this a new feature from Tassel 5?  Where does the read information come from?

Thanks again!

Sheina

[Jeff Glaubitz]

Sorry, I am brain dead today.  You are right: depth is lost.  Try instead the Tassel 4 pipeline with the -vcf option at the DiscoverySNPCallerPlugin step.

 

Or the Tassel 5 pipeline, where hdf5 (*.h5) output (including depth information) is produced by ProductionSNPCallerPlugin.  You can then use the GUI or the command line to convert to VCF:

/path/to/tassel5-standalone/run_pipeline.pl -Xmx4g -fork1 -h5 myGenos.h5 -export myGenos.vcf -exportType VCF -runfork1

 

Best,

 

Jeff

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