GATK

Tagged with #assembly
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HaplotypeCaller

I understand the HaplotypeCaller does some local assembly and realignment. Can someone expand on the parameters used during the local assembly? What is the kmer used for the assembly graph? I would like to explore the use of digital normalization prior to SNP calling to remove PCR artifacts and this information would be helpful.

HaplotypeCaller 2.4

I am getting the following error. What is the minimum read size to do assembly? 50 basepair too short?

ERROR stack trace

java.lang.IllegalStateException: Reads are too small for use in assembly. at org.broadinstitute.sting.gatk.walkers.haplotypecaller.DeBruijnAssembler.createDeBruijnGraphs(DeBruijnAssembler.java:139) at org.broadinstitute.sting.gatk.walkers.haplotypecaller.DeBruijnAssembler.runLocalAssembly(DeBruijnAssembler.java:123) at org.broadinstitute.sting.gatk.walkers.haplotypecaller.HaplotypeCaller.map(HaplotypeCaller.java:483) at org.broadinstitute.sting.gatk.walkers.haplotypecaller.HaplotypeCaller.map(HaplotypeCaller.java:132) at org.broadinstitute.sting.gatk.traversals.TraverseActiveRegions.processActiveRegion(TraverseActiveRegions.java:552) at org.broadinstitute.sting.gatk.traversals.TraverseActiveRegions.processActiveRegions(TraverseActiveRegions.java:512) at org.broadinstitute.sting.gatk.traversals.TraverseActiveRegions.traverse(TraverseActiveRegions.java:244) at org.broadinstitute.sting.gatk.traversals.TraverseActiveRegions.traverse(TraverseActiveRegions.ja at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.j at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:283 at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:1 at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:24 at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:15 at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:91)

ERROR ---------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 2.4-3-g2a7af43):
ERROR
ERROR Please visit the wiki to see if this is a known problem
ERROR If not, please post the error, with stack trace, to the GATK forum
ERROR Visit our website and forum for extensive documentation and answers to
ERROR commonly asked questions http://www.broadinstitute.org/gatk
ERROR
ERROR MESSAGE: Reads are too small for use in assembly.
ERROR ---------------------------------------------------------------------------------------

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Local reference for UG SNP-calling

The Unified Genotyper calls SNPs relative to the specified, publicly-available reference assembly.

How can I call SNPs (in many samples, with UG) relative to an in-house individual, which I have sequenced at high-coverage?

My current solution is to perform a de novo assembly on the in-house reference individual using e.g. Velvet, and then simply use the fasta as the reference for UG.

Can the publicly-available reference assembly still be useful here for speeding up the mapping and filling-in missing parts ?

My organism is Drosophila melanogaster.