About haplotypecaller (one bam to one vcf)

stellastella KoreaMember
edited November 2018 in Ask the GATK team

Dear GATK team.

Hi, I have a question.

I have seen this presentation. I obtatined this presentation file from GATK google cloud.

At the top of this figure, it is described as single sample BAM --> single sample VCF using Haplotypecaller.

[My Question] If I have one tumor sample bam file and I want to call germline variants using this tumor-only bam file, can I just do these following steps?

1. run Haplotype caller (GATK v4)
gatk HaplotypeCaller \
-R [reference_genome] \
-I [tumor-only sample] \
--dbsnp [dbsnp 151 version]\
-O [tumor-only.haplotype.vcf] \
-nct 8\

2. VariantRecalibrator (both SNP and Indel)
gatk VariantRecalibrator \
-R [reference_genome] \
-V [tumor-only.haplotype.vcf] \
-resource hapmap,known=false,training=true,truth=true,prior=15.0: hapmap_3.3.hg38.vcf \
-resource omni,known=false,training=true,truth=true,prior=12.0:/1000G_omni2.5.hg38.vcf \
-resource 1000G,known=false,training=true,truth=false,prior=10.0:/snp/1000G_phase1.snps.high_confidence.hg38.vcf \
-resource dbsnp,known=true,training=false,truth=false,prior=2.0:[dbsnp 151 version] \
-an DP -an QD -an FS -an MQRankSum -an ReadPosRankSum -an SOR \
-mode SNP \
-O [tumor-only.haplotype.recal] \
-tranches-file [tumor-only.haplotype.tranches] \
-rscript-file [tumor-only.haplotype.recal.plots.R] \

3. ApplyVQSR
gatk ApplyVQSR \
-R [reference_genome] \
-V [tumor-only.haplotype.vcf] \
-mode SNP \
-recal-file [tumor-only.haplotype.recal] \
-tranches-file [tumor-only.haplotype.tranches] \
-O [tumor-only.haplotype.recal.vcf] \
-ts-filter-level 99.5 \


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