@YungangXu @NatureBiotech Interesting question, might need to be a bit more specific. #GATK is a toolkit that cover… https://t.co/Q04BhgPgSb

@PoisonEcology GATK code overall is at https://t.co/x5Pv5EoNYU, happy to point you to specific classes if needed. U… https://t.co/l67ctR2zG5

Many thanks to @xdopazo and colleagues for hosting our #GATK workshop crew in beautiful Sevilla! Lovely location an… https://t.co/S6iXKviMNz

Methods and Algorithms

Analysis details and recommendations

ActiveRegion determination (HaplotypeCaller & Mutect2)
Allele-specific annotation and filtering of germline short variants
Assigning per-sample genotypes (HaplotypeCaller)
Base Quality Score Recalibration (BQSR)
Calculation of PL and GQ by HaplotypeCaller and GenotypeGVCFs
Calling variants on cohorts of samples using the HaplotypeCaller in GVCF mode
Evaluating the evidence for haplotypes and variant alleles (HaplotypeCaller & Mutect2)
Evaluating the quality of a germline short variant callset
Genotype Refinement workflow for germline short variants
HaplotypeCaller Reference Confidence Model (GVCF mode)
HaplotypeCaller in a nutshell
Hard-filtering germline short variants
Local re-assembly and haplotype determination (HaplotypeCaller & Mutect2)
Somatic calling is NOT simply a difference between two callsets
Variant Quality Score Recalibration (VQSR)