@davemc528 No, we don’t trim reads in any of our short read pipelines. Happy to discuss in more detail and point yo… https://t.co/QWMPXegkY0

@HollyMcQueary In general that sounds appropriate, though this might be worth discussing in more detail in our supp… https://t.co/5sa0D9iHkY

@FanBoyShi For this kind of question we'd prefer you post in the forum so we can troubleshoot in detail -- but if… https://t.co/bQqUp4ZInM

Methods and Algorithms

Reasoning and analytical details behind the tools

ActiveRegion determination (HaplotypeCaller & Mutect2)
After gCNV calling considerations
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
Difference between QUAL and GQ annotations in germline variant calling
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
The logic of joint calling for germline short variants
Variant Quality Score Recalibration (VQSR)