End-to-End Aligning and Variant Calling Examples
Paired-End BAM Input, VCF Output
| • | Enter the following input: |
dragen -f \
-r /staging/human/reference/hg19/hg19.fa.k_21.f_16.m_149 \
-b /staging/human/unsorted_SRA056922_30x_e10_50M.bam \
--enable-map-align true \
--enable-map-align-output true \
--enable-variant-caller true \
--output-directory /staging/examples/ \
--output-file-prefix SRA056922_30x_e10_50M \
--enable-duplicate-marking true
| • | Or, run /opt/edico/examples/paired_fastq_in_dupmark_bam_and_vcf_out.sh. |
If the /staging/human/unsorted_SRA056922_30x_e10_50M.bam input file for the example above is missing, run the /opt/edico/examples/paired_fastq_in_unsorted_bam_out.sh script o generate it.
Paired-End FASTQ Input, VCF Output (Default)
| • | 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 \
--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_vcf_out.sh. |
This example shows the minimum options that must be specified to perform an end-to-end run. By default, duplicate-marking is not performed and no BAM output is produced.
Paired-End Fastq Input, Sorted and Duplicate-Marked, VCF 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 \
--RGID Illumina_RGID \
--RGSM SRA056922_30x_e10_50M \
--output-directory /staging/examples/ \
--output-file-prefix SRA056922_30x_e10_50M \
--enable-duplicate-marking true
| • | Or, run /opt/edico/examples/paired_fastq_in_dupmark_vcf_out.sh. |
Paired-End FASTQ Input, Sorted BAM and VCF 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 \
--RGID Illumina_RGID \
--RGSM SRA056922_30x_e10_50M \
--output-directory /staging/examples/ \
--output-file-prefix SRA056922_30x_e10_50M \
--enable-duplicate-marking true \
--enable-map-align-output true
| • | Or, run /opt/edico/examples/sorted_bam_in_vcf_out.sh. |
Paired-End FASTQ Input, Sorted SAM and VCF 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 \
--RGID Illumina_RGID \
--RGSM SRA056922_30x_e10_50M \
--output-directory /staging/examples/ \
--output-file-prefix SRA056922_30x_e10_50M \
--enable-duplicate-marking true \
--enable-map-align-output true \
--output-format SAM
| • | Or, run /opt/edico/examples/paired_fastq_in_dupmark_sam_and_vcf_out.sh. |
Paired-End FASTQ Input, Sorted CRAM and VCF 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 \
--RGID Illumina_RGID \
--RGSM SRA056922_30x_e10_50M \
--output-directory /staging/examples/ \
--output-file-prefix SRA056922_30x_e10_50M \
--enable-duplicate-marking true \
--enable-map-align-output true \
--output-format CRAM \
| • | Or, run /opt/edico/examples/paired_fastq_in_dupmark_cram_and_vcf_out.sh. |
Paired-End FASTQ Input, Sorted BAM and VCF Output, plus Repeat Genotyping VCF
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 \
--RGID Illumina_RGID \
--RGSM SRA056922_30x_e10_50M \
--output-directory /staging/examples/ \
--output-file-prefix SRA056922_30x_e10_50M \
--enable-duplicate-marking true \
--enable-map-align-output true \
--repeat-genotype-enable true \
--repeat-genotype-specs /opt/edico/repeat-specs/hg19 \
--repeat-genotype-sex female \
--repeat-genotype-ref-fasta /staging/human/reference/h19/hg19.fa
