Please enable JavaScript.
Coggle requires JavaScript to display documents.
Genotyping and Variation Discovery - Coggle Diagram
Genotyping and Variation Discovery
Preprocessing and QC
Removing/ Filtering
Low quality reads
Duplicate reads
Realignment
Identified 🔍
GATK RealignerTargetCreator
Conduct
GATK IndelRealigner
Mapping
💢
Indels present at the ends of reads cause problems in Initial alignment.
Hence to improve mapping results
BWA
Novoalign
Stampy
MOSAIK
BFAST
Recalibration
GATK BaseRecalibrator
Adjust variables:
Machine
Sequencing Cycle
Factors affecting
Sequencing Signal
&
Base-call
Quality
Variant calling
SNV Calling
Factors for variant calls
depth of coverage
sequence context
single vs. paired-end sequencing
mapping quality
base call quality
Algorithms
📈
Statistical
Errors & Biases
Related prior information
GATK
UnifiedGenotyper
HaplotypeCaller
Samtools
mpileup
Bcftools
SOAP tool
Atlas 2
🎱
Heuristical
Minimum
read-depth
Allele frequency
Base call quality
VarScan
For contaminated samples
🔍 de novo Mutations
Direct Comparison with Ref. genome
JointSNVmix
Strelka
SomaticSniper
Individual Comparison with Ref. genome
MuTect
VarScan
Indel Calling
💢
Freq of 1 in 8000 bp
Extract indel information
♻
Scan for indels in BAM file
Built new haplotype for each indels
Realign to new haplotype
Count reads match the indels
Make indel calls
Dindel
GATK
Samtools
VCF file
Chromosome no.
Starting position of variation
Database identifier
Reference allele
Alternate allele(s)
Quality score
etc.
Structural Variant Calling
Structural variation (SV) is generally defined as a region of DNA approximately 1 kb, that include inversions and translocations or insertions and deletions.
Algorithmic Approach
Based on distance, Separate into two groups (Similar & Dissimilar)
Dissimilar read pairs clustered together based on genomic region
Filtered based on statistical assessment and reported
BreakDancer
GASV
HYDRA
PEMer (Paired-End Mapper)
SVDetec