Tagged with #genotype_given_alleles
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Hi,

I'm trying to call at known variant sites (human) in the Neanderthal (bam file), using HaplotypeCaller. I've altered the original vcfs (http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/analysis_results/integrated_call_sets/) to the following (the header is present, but I have reduced the number of columns to 8 to match the rest of the file. The ##INFO lines remain the same as the original file - I've removed them here). I have altered the ALT column to be whichever base call is not in the REF column, to allow for any alternative base to be called. I have also given QUAL, FILTER, and INFO dummy values (all periods), as I believe these columns are required, but the information is incorrect once I change the ALT variable.

##fileformat=VCFv4.1
##INFO
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO
22      16050408        rs149201999     T       A,C,G   .       .       .
22      16050612        rs146752890     C       A,T,G   .       .       .
22      16051249        rs62224609      T       A,C,G   .       .       .
22      16051347        rs62224610      G       C,T,A   .       .       . 

My command line is the following:

java -jar /path/to/GenomeAnalysisTK-2.7-2-g6bda569/GenomeAnalysisTK.jar -T HaplotypeCaller -nct 30 -I -R /path/to/human_g1k_v37.fasta --genotyping_mode GENOTYPE_GIVEN_ALLELES --alleles /path/to/cut.dummy.chr22.vcf -I /path/to/AltaiNea.hg19_1000g.22.dq.bam -o /path/to/haplotypecaller_forcedcalls_chr22.vcf

but an error comes (and I can't find anything referring to it, so I've posted!):

INFO  19:04:19,514 ProgressMeter -     22:17778431        2.83e+09   35.3 m        0.0 s     91.8%        38.5 m     3.2 m 
INFO  19:04:21,267 GATKRunReport - Uploaded run statistics report to AWS S3 
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR stack trace 
java.lang.IllegalStateException: Cannot trim a Haplotype without containing GenomeLoc
        at org.broadinstitute.sting.utils.haplotype.Haplotype.trim(Haplotype.java:114)
        at org.broadinstitute.sting.gatk.walkers.haplotypecaller.HaplotypeCaller.trimActiveRegion(HaplotypeCaller.java:983)
        at org.broadinstitute.sting.gatk.walkers.haplotypecaller.HaplotypeCaller.assembleReads(HaplotypeCaller.java:875)
        at org.broadinstitute.sting.gatk.walkers.haplotypecaller.HaplotypeCaller.map(HaplotypeCaller.java:750)
        at org.broadinstitute.sting.gatk.walkers.haplotypecaller.HaplotypeCaller.map(HaplotypeCaller.java:140)
        at org.broadinstitute.sting.gatk.traversals.TraverseActiveRegions$TraverseActiveRegionMap.apply(TraverseActiveRegions.java:708)
        at org.broadinstitute.sting.gatk.traversals.TraverseActiveRegions$TraverseActiveRegionMap.apply(TraverseActiveRegions.java:704)
        at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler$ReadMapReduceJob.run(NanoScheduler.java:471)
        at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
        at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334)
        at java.util.concurrent.FutureTask.run(FutureTask.java:166)
        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
        at java.lang.Thread.run(Thread.java:724)
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A GATK RUNTIME ERROR has occurred (version 2.7-2-g6bda569):
##### ERROR
##### ERROR This might be a bug. Please check the documentation guide to see if this is a known problem.
##### ERROR If not, please post the error message, 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: Cannot trim a Haplotype without containing GenomeLoc
##### ERROR ----------------------------------------------------------------------

Any suggestions welcome!

Thanks,

Anna