Genomic data includes whole-genome resequencing data from the HudsonAlpha Institute for Biotechnology, Alabama for 384 samples for accessions from the sorghum Bioenergy Association Panel (BAP) and genotyping-by-sequencing (GBS) data from Kansas State University for 768 samples from a population of sorghum recombinant inbred lines (RIL).
Danforth Center genomics pipeline
Outlined below are the steps taken to create a raw vcf file from paired end raw FASTQ files. This was done for each sequenced accession so a HTCondor DAG Workflow was written to streamline the processing of those ~200 accessions. While some cpu and memory parameters have been included within the example steps below those parameters varied from sample to sample and the workflow has been honed to accomodate that variation. This pipeline is subject to modification based on software updates and changes to software best practices.
CoGe has integrated the tools that make up the Danforth Center’s variant calling pipeline into their easy point and click GUI, allowing users to reproduce a majority of the TERRA SNP analysis. Below, we detail how to run sequence data through CoGe’s system.
Select Data: to use the TERRA data click Community Data or choose from CoGe’s other data options.
Select Options: This outlines CoGe’s choices for data processing and analysis. To reproduce pipeline used to create the TERRA SNPs, you can reference the exact tools and parameters used in the Danforth analysis above and enter the appropriate values into their equivalent drop downs or fields.
For the TERRA SNP the following were used:
Read Type: Paired-end
BBDuk parameters: k=23, mink=11, hdist=1, check mark both tpe and tbo, qtrim=rl, trimq=20, minlen=20, set trim adapters to both ends
BWA-MEM parameters: check mark -M, fill in Read Groups ID (identifier), PL (sequence platform), LB (library prep), SM (sample name)
Check mark Enable which expands this section
Method: GATK HaplotypeCaller (single-sample GVCF) using the default parameters but you can choose to use Realign reads around INDELS
Checkmark both options to add results to your notebook and receive an email when pipeline has completed.
Describe Experiment: Enter an experiment name (required), your data processing version ie 1 for first time, Source if using TERRA Data, it’s TERRA (required), and Genome (required and if you start typing it will find your loaded genome but be sure to verify version and id .)