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# HaplotypeCaller --fullHaplotype not outputting full haplotype

Posts: 1Member
edited August 2012

I am also having a problem with HaplotypeCaller - when I set the flag to print out full haplotypes, no haplotype files are created. Here is my command:

java -jar /home/chodon/applications/GATK/GenomeAnalysisTK.jar -T HaplotypeCaller -R /home/chodon/comb_eny/abyss/final_contigs/A2/Assembly.fasta -I /home/chodon/comb_eny/abyss/final_contigs/A2/bowtie2_out/A2.sorted.bam --fullHaplotype --ignoreLaneInfo -o /home/chodon/comb_eny/abyss/final_contigs/A2/GATK_haplo2.out


Any help is much appreciated! Thanks, C

Post edited by Geraldine_VdAuwera on
Tagged:

• Posts: 122GATK Developer mod

Hi there,

The --fullHaplotype option is an experimental and unsupported command line argument for the HaplotypeCaller. In version 2.1 this will be reflected as an "Advanced" option in the documentation.

However, if you are willing to experiment with this you need to add --genotypeFullActiveRegion to your command line and run it again. I would be very curious to hear what you think of how the output is formatted and if you find the argument useful at all.

Cheers,

• Posts: 1Member

When I added --genotypeFullActiveRegion, full command here:

java -jar /home/chodon/applications/GATK/GenomeAnalysisTK.jar -T HaplotypeCaller -R /home/chodon/comb_eny/abyss/final_contigs/A2/Assembly.fasta -I /home/chodon/comb_eny/abyss/final_contigs/A2/bowtie2_out/A2.sorted.bam --genotypeFullActiveRegion --fullHaplotype --ignoreLaneInfo -o /home/chodon/comb_eny/abyss/final_contigs/A2/GATK_haplo3.out

I got an error message: Code exception - here is the stack trace

##### ERROR stack trace

Thanks again! C

• Posts: 122GATK Developer mod

Ah, I see what the problem is but unfortunately you'll have to wait until we release version 2.1 (targeted for next week) to get the fix. Thanks for letting me know that someone is interested in this command line option though!

• Posts: 4Member

Hi, I am trying the same things, and I have version 2.1. I get an error that says "Unexpected bases in allele bases"