gVCF and Genotyping Examples

Paired-End FASTQ Input, gVCF Output

•

Enter the following input:

dragen -f \
-r /staging/human/reference/hg19/hg19.fa.k_21.f_16.m_149 \
-1 /staging/examples/reads/SRA056922_30x_shuffle16k_e10_50M_1.fastq.gz \
-2 /staging/examples/reads/SRA056922_30x_shuffle16k_e10_50M_2.fastq.gz \
--enable-variant-caller true \
--vc-emit-ref-confidence GVCF \
--RGID Illumina_RGID \
--RGSM SRA056922_30x_e10_50M \
--output-directory /staging/examples/ \
--output-file-prefix SRA056922_30x_e10_50M

•

Or, run /opt/edico/examples/paired_fastq_in_gVCF_out.sh.

Join Calling with gVCF Input

•

Enter the following input:

dragen -f \
-r /staging/human/reference/hg19/hg19.fa.k_21.f_16.m_149 \
--enable-joint-genotyping true \
--output-directory /staging/examples/ \
--output-file-prefix Joint_SRA056922_30x_e10_50M \
--variant /staging/examples/SRA056922_30x_e10_50M.gvcf.gz

•

Or, run /opt/edico/examples/single_gVCF_in_jointVCF_out.sh.

Pedigree-Based Joint Genotyping with Three gVCF Files and a Pedigree File Input, Joint-Genotyped VCF Output

One Step Population-Based Joint Genotyping with gVCF Input, Joint-Genotyped Multisample Output

Two Step Population-Based Joint Genotyping with gVCF List Input, Joint-Genotyped Multisample VCF Output

The first step generates a multisample VCF as output using a gVCF list as input and the following command line option.

dragen -f \
--enable-gvcf-genotyper true \
--enable-map-align false \
--variant-list ${GVCF_LIST} \
--ht-reference ${FASTA_REF} \
--intermediate-results-dir ${TEMP_DIR} \
--output-directory ${OUTPUT_DIR} \
--output-file-prefix ${COHORT_NAME}

The second step generates a joint-genotyped multisample VCF using the multisample VCF produced from step one as input and the following command line option. To specify the multisample VCF, use --variant.

dragen -f \
--enable-joint-genotyping true \
--variant ${MULTISAMPLE_VCF} \
--ref-dir ${FASTA_REF} \
--output-directory ${OUTPUT_DIR}\
--output-file-prefix ${COHORT_NAME}.joint_genotyped

Joint-calling modes, with associated input files and command line options.
VCF to generate	Population joint-called multisample gVCF	Family joint-called multisample gVCF	Population joint-called multisample VCF	Family joint-called multisample VCF
Input file	Multisample combined gVCF file	Multisample combined gVCF file	Multi-sample combined gVCF file or X individual gVCF files	Multi-sample combined gVCF file or X individual gVCF files
Use pedigree file	No	Yes	No	Yes
Command line option	--enable-joint-genotyping true --enable-multi-sample-gvcf=TRUE	--enable-joint-genotyping true --enable-multi-sample-gvcf=TRUE --pedigree-file file.ped	--enable-joint-genotyping true	--enable-joint-genotyping true --pedigree-file file.ped