WGS_example - Githubissues

kjh918 / WGS

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WGS_example #1

Open kjh918 opened 4 years ago

kjh918 commented 4 years ago

WGS (Whole Genome Sequencing)

kjh918 commented 4 years ago

STEP 0

Raw Data Download
QC and Trim

kjh918 commented 4 years ago

STEP 1

Map to Reference (BWA mem)

kjh918 commented 4 years ago

STEP 2

Mark Duplicates

kjh918 commented 4 years ago

STEP 3

Base Quality Score Recalibaration (first step)
Base Quality Score Recalibaration (second step)

kjh918 commented 4 years ago

STEP 4

Calling variants for all samples with HaplotypeCaller
Applying GenotypeGVCFs

kjh918 commented 4 years ago

STEP 5

Extracting the SNPs and Indels with SelectVariants
Applying hard-filtering on the SNPs and Indels with VariantFiltration
Merge the file for SNPs and Indels with MergeVcfs

kjh918 commented 4 years ago

ADD

Annotation using Annovar
Functional annotation with snpEff
SnpSift Annotate (dbSNP)