Asked 6 months ago. Note also that the system requirements for old versions may be different than what is documented for the current version; we do not document these explicitly here but you may find that information in the Version History. Here is the stack trace: It only takes a minute to sign up. What would happen if I used homozygous sample and set "--maxNumHaplotypesInPopulation" to 1 how does it choose the 1 haplotype and what happens to reads that don't match that haplotype? Post as a guest Name. Can a GATK tool automatically name detected variants, i. 
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Whenever possible, you should always use the latest and greatest version of GATK. I presume this will still work, but I can't say I've ever tried.
haplotypecaller — GATK-Forum
gxtk I do this for mark duplicates removed but for multimappers I would like to know how you define so I can do the same. Recent version of GATK v3. We'd especially love gxtk get some feedback from people who work with non-diploids on a regular basis, so we're hoping that some of you microbiologists and assorted plant scientists will take it out for a spin and let us know how it behaves in your hands.
gati I how ever know that this should be the same reference used for the alignment. Bioinformatics Stack Exchange is a question and answer site for researchers, developers, students, teachers, and end users interested in bioinformatics. That caused issues with the bam 'bins', so we had to run the htsjdk.
bam - Variant calling without matched normal sample - Bioinformatics Stack Exchange
If it is just because of the different setting of "-minPruning 3" and "-minPruning 2", I would say the setting of "-minPruning" is critical for the final results so a guideline of how to set the "-minPruning" based on the sequencing depth will be important.
Queue Queue 3. I wonder if something went wrong with the bam processing. Contig '20' does not match any contig in the GATK sequence dictionary derived from the reference; are you sure you are using the correct reference fasta file? Browsing All Articles Articles. Here is the stack trace:. I get the error message: The best answers are voted up and rise to the top. Strange results generated from HaplotypeCaller when comparing "-minPruning 3" with "-minPruning 2".
I have downloaded the hg19 from ftp: To look up arguments and default values for older versions, you will need to use the command-line help system, which you can invoke using --help.
Browse the Latest Snapshot. But, I don't know start from where? I should mention, Calling SNV and indel in many tools returns vcf but I called copy number by varscan that did not return.
How I can get all 3 class of genotype in the output? Asked 6 months ago. I narrowed the gwtk down to 15 reads see attached files. Can a GATK tool automatically name detected variants, i. We make these available for purposes such as comparative testing and project consistency, but you should be aware that these old versions are completely unsupported and that if you choose to use them, you do so at your own risk!
Someone know why this is caused and maybe how to solve this? The BAM file was produced gati to the best practice guide.
And here are the program args for one of them: We are analysing monozygotic twins while using the HaplotypeCaller but we see some weird gakt. I encountered a NullPointerException in 3.
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I am wondering what exactly happens for this locus so I check this locus using IGV. This new feature, which we're calling "omniploidy", is technically still under development, but we think it's mature enough for the more adventurous to try out as a beta test ahead of the next official release.
Just wondering is it normal considering the different setting of "-minPruning 3" and "-minPruning 2"or is it just a bug? You can see it is quite different for the results in terms of gark final genotyping call and the sequencing depth "DP" tag generated from "-minPruning 3" and "-minPruning 2" setting.
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