Germline variant calling (GATK4)

Modified on Sat, 2 Sep, 2023 at 2:12 PM

Variant calling workflow and Report page overview

Germline variant calling starts with the BAM file produced by our Alignment/QC pipeline, variants are called using HaplotypeCaller from GATK, and then annotated using snpEff. The report page provides an interactive table to browse and filter the raw variant calls and summary statistics are available as well.

Results

Table

-an interactive table to browse and filter called variants

Analytics

-summary statistics of the number and types of variants detected

Output Files

HaploTypeCaller (GATK4)
gatk_haplotypecaller/<SAMPLE_NAME>.<genome>.variants.vcf.gz.tbi

-index file of raw variant call VCF file
gatk_haplotypecaller/<SAMPLE_NAME>.<genome>.variants.vcf.gz

-compressed raw variant call file in VCF format
SnpEff
snpeff/<SAMPLE_NAME>.<genome>.variants.w_AF.annotated.vcf.gz.tbi

-index file of annotated VCF file
snpeff/<SAMPLE_NAME>.<genome>.variants.w_AF.annotated.vcf.gz

-compressed, annotated variant call file in VCF format
snpeff/<SAMPLE_NAME>.<genome>.variants.w_AF.snpEff_summary.html

-summary file of variant calls and annotations from snpEff

Report
report/<SAMPLE_NAME>.<genome>.variants.w_AF.annotated.xls

-annotated variant calls in xls format