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      Genome-Wide Association Studies

Introduction and Lectures
Intro to the Workshop and Core
Dr. Anthony Musolf Talk
What is Bioinformatics/Genomics?
Cheat Sheets
Software and Links
Logging In
Cluster Computing
Data Reduction
Files and Filetypes
Project setup
Preprocessing raw data
Alignment with BWA
Variant calling using GATK
Comparison of freebayes, GATK, and deepvariant output
Data Analysis
Plink Step by Step TDT
Plink Step by Step TDT (solutions)
wAnnovar Annotation
Plink Step by Step (Non FBAT excercise)
Setup in R
GWAS Visualization
Closing thoughts
Workshop Photos
Github page
Biocore website

Comparison of freebayes, gatk, and deepvariant outputs

freebayes, gatk, and deepvariant were run on the full chr22 dataset. Here is the command for freebayes:

module load freebayes
freebayes --bam-list bamlist.txt --fasta-reference ref/chr22.fa --vcf 03-freebayes/fb.ALL.vcf

where bamlist.txt is a file containing the names of the 3 bam files.

Here are the commands for deepvariant:

module load deepvariant

singularity exec --nv -B /usr/lib/locale/:/usr/lib/locale/ -H /share/workshop/gwas_workshop/joshi $DEEPVARIANT_IMG_PATH/deepvariant-1.1.0-gpu.simg /opt/deepvariant/bin/run_deepvariant --logging_dir logs --model_type WGS --output_gvcf 03-deepvariant/SL378587.gvcf --output_vcf 03-deepvariant/SL378587.vcf --reads 02-BWA/SL378587/SL378587.pe.bam --ref ref/chr22.fa --num_shards 10

singularity exec --nv -B /usr/lib/locale/:/usr/lib/locale/ -H /share/workshop/gwas_workshop/joshi $DEEPVARIANT_IMG_PATH/deepvariant-1.1.0-gpu.simg /opt/deepvariant/bin/run_deepvariant --logging_dir 03-deepvariant/SL378588_logs --model_type WGS --output_gvcf 03-deepvariant/SL378588.gvcf --output_vcf 03-deepvariant/SL378588.vcf --reads 02-BWA/SL378588/SL378588.pe.bam --ref ref/chr22.fa --num_shards 10

singularity exec --nv -B /usr/lib/locale/:/usr/lib/locale/ -H /share/workshop/gwas_workshop/joshi $DEEPVARIANT_IMG_PATH/deepvariant-1.1.0-gpu.simg /opt/deepvariant/bin/run_deepvariant --logging_dir 03-deepvariant/SL378589_logs --model_type WGS --output_gvcf 03-deepvariant/SL378589.gvcf --output_vcf 03-deepvariant/SL378589.vcf --reads 02-BWA/SL378589/SL378589.pe.bam --ref ref/chr22.fa --num_shards 10

Then the three gvcf files were combined into into a single bcf (binary vcf) file using glnexus_cli:

glnexus_cli --config DeepVariantWGS 03-deepvariant/SL37858*.gvcf > 03-deepvariant/deepvariant.ALL.bcf

and finally converting the bcf to vcf:

module load bcftools
bcftools view deepvariant.ALL.bcf > deepvariant.ALL.vcf

The gatk commands were the ones from the course.

Here are the numbers of variants found per software (after filtering out low quality variants):

freebayes 110340
GATK 127217
deepvariant 96581

Looking at just the variant call positions, here is the venn diagram of shared positions:

venn diagram

Filtering for just SNPs gives us this venn diagram:

venn diagram

And finally, looking at identical genotype calls give us this:

venn diagram

You can see that almost all of the SNP calls are the same, which is to be expected.