call variants for a single sample using HC

Answers

• Sheila Broad InstituteMember, Broadie ✭✭✭✭✭

  January 2015 Accepted Answer

  @Usha
  Hi,
  If you are simply calling variants on a single sample, you can use the first command you posted. The second command you posted is for joint calling on many samples. Please read more about it here: http://gatkforums.broadinstitute.org/discussion/4017/what-is-a-gvcf-and-how-is-it-different-from-a-regular-vcf

  https://www.broadinstitute.org/gatk/guide/article?id=3893

  -Sheila

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• Usha Member ✭

  February 2015

  Thanks Sheila.
  Once we have the recalibrated_variants.vcf how do you annotate the vcf file with dbSNP id’s?
  Do we need to use snpeff or Annovar?
  If yes, has anyone used Annovar to annotate the dbSNP id's? what are the steps needed for that?

  Thanks.

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• Geraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

  February 2015 edited February 2015

  You can get HC to annotate dbSNP ids for you while doing the calling; see the -dbsnp argument. To do it in post-processing you can use Variant Annotator.

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• Usha Member ✭

  February 2015

  Thanks Geraldine.

  Just want to make sure I was doing this correctly. I was using the one posted in one of the GATK presentations. Is this correct?

  java -Xmx6g -jar $GATK/GenomeAnalysisTK.jar \
  -T VariantRecalibrator \
  -R ${reference} \
  -input ${result}/raw_variants.vcf \
  -resource:hapmap,known=false,training=true,truth=true,prior=15.0 ${hapmap} \
  -resource:omni,known=false,training=true,truth=false,prior=12.0 ${omni} \
  -resource:1000G,known=false,training=true,truth=false,prior=10.0 ${phase1snp} \
  -resource:dbsnp,known=true,training=false,truth=false,prior=2.0 ${dbsnp} \
  -an DP \
  -an QD \
  -an FS \
  -an MQRankSum \
  -an ReadPosRankSum \
  -mode SNP \
  -tranche 100.0 \
  -tranche 99.9 \
  -tranche 99.0 \
  -tranche 90.0 \
  -numBad 1000 \
  -recalFile ${result}/recalibrate_SNP.recal \
  -tranchesFile ${result}/recalibrate_SNP.tranches \
  -rscriptFile ${result}/recalibrate_SNP_plots.R

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• Sheila Broad InstituteMember, Broadie ✭✭✭✭✭

  February 2015 Accepted Answer

  @Usha
  Hi,

  That is fine if you are using VariantRecalibrator, but to get dbSNP ids you need to use Variant Annotator
  https://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_gatk_tools_walkers_annotator_VariantAnnotator.php#--dbsnp

  -Sheila

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• Geraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

  February 2015 Accepted Answer

  I think we no longer require specifying -numBad. You should check the FAQ on VQSR parameters. It lists the exact Best Practices parameters.

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• Usha Member ✭

  February 2015

  Thanks Sheila & Geraldine.

  Can we use Variant Annotator directly without using snpeff?

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• Geraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

  February 2015 Accepted Answer

  Yes of course -- snpeff is used for a different kind of annotation.

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