3. Sample Sheet Setup

Use the following as general guide to determine the columns you need to include in your sample.csv metadata file to set up your structural variant calling run.

3.1. Choosing your sample sheet layout¶

Depending on what scenario best describes your data implement the recommended columns. Below each example is a corresponding boolean value for what the use_custom_reference directive should be in the config.yaml file.

3.1.1. Single lane local reads and NCBI refSeq reference genome¶

Run,BioSample,LibraryName,refGenome,fq1,fq2
sample1,1,lib_sample1,GCF_XXXXXXXXX.X,/path/to/sample1_lane1_1.fastq.gz,/path/to/sample1_lane1_2.fastq.gz

use_custom_reference: False

3.1.2. Single lane local reads and a custom reference¶

Run,BioSample,LibraryName,refGenome,refPath,fq1,fq2
sample1,1,lib_sample1,GCF_XXXXXXXXX.X,/path/to/custom/reference/REF_NAME.fna,/path/to/sample1_lane1_1.fastq.gz,/path/to/sample1_lane1_2.fastq.gz

use_custom_reference: True

3.1.3. Multi lane local reads and NCBI refSeq reference genome¶

Run,BioSample,LibraryName,refGenome,fq1,fq2
sample1,1,lib_sample1,GCF_XXXXXXXXX.X,/path/to/sample1_lane1_1.fastq.gz,/path/to/sample1_lane1_2.fastq.gz
sample1,2,lib_sample1,GCF_XXXXXXXXX.X,/path/to/sample1_lane2_1.fastq.gz,/path/to/sample1_lane2_2.fastq.gz
sample2,1,lib_sample2,GCF_XXXXXXXXX.X,/path/to/sample2_lane1_1.fastq.gz,/path/to/sample2_lane1_2.fastq.gz
sample2,2,lib_sample2,GCF_XXXXXXXXX.X,/path/to/sample2_lane2_1.fastq.gz,/path/to/sample2_lane2_2.fastq.gz

use_custom_reference: False

3.1.4. Multi lane local reads and a custom reference¶

Run,BioSample,LibraryName,refGenome,refPath,fq1,fq2
sample1,1,lib_sample1,GCF_XXXXXXXXX.X,/path/to/custom/reference/REF_NAME.fna,/path/to/sample1_lane1_1.fastq.gz,/path/to/sample1_lane1_2.fastq.gz
sample1,2,lib_sample1,GCF_XXXXXXXXX.X,/path/to/custom/reference/REF_NAME.fna,/path/to/sample1_lane2_1.fastq.gz,/path/to/sample1_lane2_2.fastq.gz
sample2,1,lib_sample2,GCF_XXXXXXXXX.X,/path/to/custom/reference/REF_NAME.fna,/path/to/sample2_lane1_1.fastq.gz,/path/to/sample2_lane1_2.fastq.gz
sample2,2,lib_sample2,GCF_XXXXXXXXX.X,/path/to/custom/reference/REF_NAME.fna,/path/to/sample2_lane2_1.fastq.gz,/path/to/sample2_lane2_2.fastq.gz

use_custom_reference: True

3.1.5. Single lane with custom reference and user provided BAM files¶

Run,BioSample,LibraryName,refGenome,refPath,bamPath,baiPath
sample1,1,lib_sample1,GCF_XXXXXXXXX.X,REF_NAME.fna,/path/to/your/sample1.bam,/path/to/your/sample1.bam.bai
sample2,1,lib_sample2,GCF_XXXXXXXXX.X,REF_NAME.fna,/path/to/your/sample2.bam,/path/to/your/sample2.bam.bai

use_custom_reference: True

For further details on executing the workflow from BAM files refer to the guide here.