Somatic Variant calling (GATK4-Mutect2

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

Variant calling workflow and Report page overview

Somatic variant calling starts with the BAM files produced by our Alignment/QC pipeline, variants are called using Mutect2 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

Mutect2 (GATK4)
gatk_mutect/<SAMPLE_NAME>.<genome>.variants.vcf.gz.tbi

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

-compressed raw variant call file in VCF format
FilterMutectCalls (GATK4)
gatk_mutect_filter/<SAMPLE_NAME>.<genome>.variants.filtered.vcf.gz

-compressed, filtered variant call file in VCF format
gatk_mutect_filter/<SAMPLE_NAME>.<genome>.variants.filtered.vcf.gz.tbi

-index file of filtered variant call file
SnpEff
snpeff/<SAMPLE_NAME>.<genome>.variants.filtered.w_AF.annotated.vcf.gz.tbi

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

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

-summary file of variant calls and annotations from snpEff

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

-annotated variant calls in xls format