Variant Calling Only Examples

The variant calling only examples show how you can pass an existing aligned BAM or CRAM file directly to the DRAGEN Variant Caller. By default, the BAM/CRAM file is passed through the sorting stage prior to variant calling.

To duplicate mark your BAM file before running the DRAGEN Variant Caller, you need to use a separate tool. The DRAGEN Duplicate Marker depends on information provided by the Mapper/Aligner that does not exist in BAM files. To take advantage of the DRAGEN Duplicate Marker, use DRAGEN in end-to-end mode.

The BAM/CRAM files that are used as input to these example commands are not included in the example data set. They are generated by example commands in Alignment Only Examples.

Unsorted BAM Input, VCF Output (Default)

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Enter the following input:

dragen -f \
-r /staging/human/reference/hg19/hg19.fa.k_21.f_16.m_149 \
-b /staging/examples/unsorted_SRA056922_30x_e10_50M.bam \
--enable-variant-caller true \
--output-directory /staging/examples/ \
--output-file-prefix unsorted_output_SRA056922_30x_e10_50M \
--enable-map-align false

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

Sorted BAM Input, VCF Output

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Enter the following input:

dragen -f \
-r /staging/human/reference/hg19/hg19.fa.k_21.f_16.m_149 \
-b /staging/examples/SRA056922_30x_e10_50M.bam \
--enable-variant-caller true \
--output-directory /staging/examples/ \
--output-file-prefix sorted_output_SRA056922_30x_e10_50M \
--enable-map-align false
--enable-sort false

•

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

Sorted CRAM Input, VCF Output

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Enter the following input:

dragen -f \
-r /staging/human/reference/hg19/hg19.fa.k_21.f_16.m_149 \
--enable-variant-caller true \
--output-directory /staging/examples/ \
--output-file-prefix sorted_output_SRA056922_30x_e10_50M \
--enable-sort false \
--enable-map-align false \
--cram-input /staging/examples/SRA056922_30x_e10_50M.cram

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