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call variants for a single sample using HC
Usha
Member ✭
I am using HC and the following command to call variants for a single sample using the genotyping_mode DISCOVERY. This is still running.
java -Xmx6g -jar $GATK/GenomeAnalysisTK.jar \
-T HaplotypeCaller \
-R ${reference} \
-I ${result}/reduced_reads.bam \
-L chr21 \
--genotyping_mode DISCOVERY \
-stand_emit_conf 10 \
-stand_call_conf 30 \
-o ${result}/raw_variants.vcf
Came across another command in Best Practices document.
java–jarGenomeAnalysisTK.jar
–T HaplotypeCaller\
–R human.fasta \
–I sample1.bam \
–o sample1.g.vcf \
–ERC GVCF\
-‐-‐variant_index_typeLINEAR\
-‐-‐variant_index_parameter 128000
Can you please let me know the difference and what command do I need to call variants for a single sample?
Output is a gvcf which is an intermediate step followed by VCF file.
Best Answers
-
Sheila
Broad Institute admin
@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-vcfhttps://www.broadinstitute.org/gatk/guide/article?id=3893
-Sheila
-
Sheila
Broad Institute admin
@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
-
Geraldine_VdAuwera
Cambridge, MA admin
I think we no longer require specifying -numBad. You should check the FAQ on VQSR parameters. It lists the exact Best Practices parameters.
-
Geraldine_VdAuwera
Cambridge, MA admin
Yes of course -- snpeff is used for a different kind of annotation.
Answers
@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
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.
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.
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
@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
I think we no longer require specifying -numBad. You should check the FAQ on VQSR parameters. It lists the exact Best Practices parameters.
Thanks Sheila & Geraldine.
Can we use Variant Annotator directly without using snpeff?
Yes of course -- snpeff is used for a different kind of annotation.