HaplotypeCaller rs annotation

flescaiflescai Posts: 61Member ✭✭

Hi there,
I'm running now the new GATK 2.2-2 version and I noticed an issue with HaplotypeCaller I had in the previous version I was using.
Despite adding the dbSNP ROD to the walker, the emitted VCF doesn't contain rs names in the name field.
On the contrary, UnifiedGenotyper annotates the variants with the appropriate names.

In my .scala code I wrote:

 class HaplotypeCallerArguments (t: Target) extends HaplotypeCaller with UNIVERSAL_GATK_ARGS {
   this.reference_sequence = qscript.referenceFile
   this.intervals = if (qscript.intervals == null) Nil else List(qscript.intervals)
   // Set the memory limit to 6 gigabytes on each command.
   this.memoryLimit = 6
   this.input_file :+= qscript.bamFile
   this.D = qscript.dbSNP_b37
 }

and that is correctly reflected when queue launches the job as

 INFO  16:07:30,655 FunctionEdge - Starting:  'java'  '-Xmx6144m'  '-XX:+UseParallelOldGC'  '-XX:ParallelGCThreads=4'  '-XX:GCTimeLimit=50'  '-XX:GCHeapFreeLimit=10'  '-Djava.io.tmpdir=/SAN/biomed/analysis/tmp'  '-cp' '/share/apps/genomics/Queue-2.2-2-gf44cc4e/Queue.jar'  
 'org.broadinstitute.sting.gatk.CommandLineGATK'  '-T' 'HaplotypeCaller'  '-I' '/SAN/biomed/analysis/recal.list'  '-L' '/SAN/biomed/analysis/.queue/scatterGather/HaplotypeCaller-sg/temp_016_of_300/scatter.intervals'  '-R' '/share/apps/genomics/reference/human_g1k_v37.fasta'  
 '-l' 'INFO'  '-o' '/SAN/biomed/analysis/.queue/scatterGather/HaplotypeCaller-sg/temp_016_of_300/comparisonHC.raw.vcf' '-D' '/share/apps/genomics/reference/gatkresources_hg19_1.5/ftp.broadinstitute.org/bundle/1.5/b37/dbsnp_135.b37.vcf'  

However, my VCF still looks like

grep -v \# HC.raw.vcf | cut -f 1,2,3,4,5 | more
1   762273  .   G   A
1   865738  .   A   G
1   866319  .   G   A
1   866511  .   C   CCCCT
1   871042  .   C   CA
1   874734  .   C   T

Am I doing something wrong?
It would be quite time consuming to launch VariantAnnotation if not necessary, as I understand now the covariates used by VQSR are already emitted by the caller.

thanks,
Francesco

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Best Answer

  • rpoplinrpoplin Posts: 122GATK Developer mod
    Answer ✓

    Unfortunately the HaplotypeCaller can't annotate the rsIDs yet. We'll work on getting this added for the next release. Thanks for letting us know that you need this functionality.

    Cheers,

Answers

  • rpoplinrpoplin Posts: 122GATK Developer mod
    Answer ✓

    Unfortunately the HaplotypeCaller can't annotate the rsIDs yet. We'll work on getting this added for the next release. Thanks for letting us know that you need this functionality.

    Cheers,

  • treddytreddy Posts: 1Member

    I was wondering if this has been updated? I've been calling HaplotypeCaller with the --dbsnp command, but none of the SNPs in my output have IDs, even though they overlap and have the same genotypes as ones in my dbsnp file. I'm using GATK 2.5.2

  • CarneiroCarneiro Posts: 274Administrator, GATK Developer admin

    Not yet, it is a known limitation of the tool that we have listed as a todo but we haven't gotten to it yet.

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