Alignment Only Examples

All the variations for performing alignment shown in these examples can be used in the end-to-end case as well.

Map/Align Single-Ended FASTQ Input, Sorted BAM 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_rand1_100K.fastq \
--output-directory /staging/examples/ \
--output-file-prefix SRA056922_30x_rand1_100K \
--RGID DRAGEN_RGID \
--RGSM DRAGEN_RGSM \

•

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

Map/Align Single-ended FASTQ input, Sorted, Duplicate-Marked BAM 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_rand1_100K.fastq \
--output-directory /staging/examples/ \
--output-file-prefix SRA056922_30x_rand1_100K_dup_marked \
--enable-duplicate-marking true \
--RGID DRAGEN_RGID \
--RGSM DRAGEN_RGSM

•

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

Map/Align Paired-End FASTQ Input, Sorted BAM 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 \
--output-directory /staging/examples/ \
--output-file-prefix SRA056922_30x_e10_50M \
--RGID DRAGEN_RGID \
--RGSM DRAGEN_RGSM

•

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

Map/Align Paired-End FASTQ Input, Sorted CRAM 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 \
--output-directory /staging/examples/ \
--output-file-prefix SRA056922_30x_e10_50M \
--output-format CRAM \
--RGID DRAGEN_RGID \
--RGSM DRAGEN_RGSM

•

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

Map/Align Paired-End FASTQ Input, Sorted Uncompressed BAM Output

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 \
--output-directory /staging/examples/ \
--output-file-prefix uncompressed_SRA \
--enable-bam-compression false \
--RGID DRAGEN_RGID \
--RGSM DRAGEN_RGSM

Map/Align Paired-End FASTQ Input, Sorted SAM 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 \
--output-directory /staging/examples/ \
--output-file-prefix SRA056922_30x_e10_50M \
--output-format SAM \
--RGID DRAGEN_RGID \
--RGSM DRAGEN_RGSM

•

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

Map/Align Paired -End FASTQ Input, UN-Sorted BAM 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 \
--output-directory /staging/examples/ \
--output-file-prefix unsorted_SRA056922_30x_e10_50M \
--enable-sort false \
--RGID DRAGEN_RGID \
--RGSM DRAGEN_RGSM

•

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

Map/Align Interleaved Paired-Ended FASTQ Input, BAM 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_PE_30x_rand1_10K_interleaved.fastq \
--interleaved \
--output-directory /staging/examples/ \
--output-file-prefix SRA056922_PE_30x_rand1_10K_interleaved \
--RGID DRAGEN_RGID \
--RGSM DRAGEN_RGSM

•

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