WGS只能call SNV、CNV、SV和mtDNA变异？

Inference of ploidy and heterozygosity structure using whole genome sequencing data
https://github.com/KamilSJaron/smudgeplot

STR
https://github.com/tfwillems/HipSTR
https://github.com/gymreklab/GangSTR
https://github.com/mgymrek/lobstr-code

HLA
https://github.com/DiltheyLab/HLA-LA
https://github.com/FRED-2/OptiType
https://github.com/warrenlr/HLAminer

fetal trisomies and smaller CNV
https://github.com/VUmcCGP/wisecondor

Somatic copy number analysis
https://github.com/cancerit/ascatNgs

Complex structural variant detection
https://github.com/SUwonglab/arcsv

uses Read Pair and Split Read methods to identify structural variants in paired-end WGS data
https://github.com/njdbickhart/RAPTR-SV

detection of copy number variants (CNVs) on human genomes from next generation sequence data, utilizing information from read depth of short reads and SNV heterozygosity.
https://github.com/igm-team/ERDS

Estimating tumor fraction in cell-free DNA from ultra-low-pass whole genome sequencing.
https://github.com/broadinstitute/ichorCNA

analysis of structural variation in genomes
https://github.com/nhansen/SVanalyzer

Analysis of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) in cancer
https://github.com/gavinha/TitanCNA

Allele-Specific Quantification of Structural Variations in Cancer Genomes
https://github.com/ma-compbio/Weaver

fast and accurate SNP genotyping from whole genome sequencing data for bedside diagnostics
https://github.com/medvedevgroup/vargeno

A bioinformatics pipeline to analyze mtDNA from NGS data
https://github.com/mitoNGS/MToolBox

calculating telomere length
https://github.com/zd1/telseq

Functions and methods for working with VCFs in the ploidyverse
https://github.com/ploidyverse/ploidyverseVcf

Deconvolving tumor purity and ploidy by integrating copy number alterations and loss of heterozygosity
https://github.com/uci-cbcl/PyLOH