Tool Reference

Tools By Category

Category	Tool
FASTQ/BAM Processing	applybqsr bam2fq bamsort bqsr fq2bam (FQ2BAM + BWA-MEM) fq2bamfast (FQ2BAM + BWA-MEM) fq2bam_meth markdup minimap2 (Beta)
Variant Calling	deepvariant deepvariant_germline germline (GATK Germline Pipeline) haplotypecaller mutectcaller pacbio_germline (Beta) postpon prepon somatic (Somatic Variant Caller)
RNA	rna_fq2bam starfusion
Quality Control	bammetrics collectmultiplemetrics
Variant Processing	dbsnp
GVCF Processing	genotypegvcf indexgvcf