Question: DNAseq pipeline steps
23 months ago by
shuksi1984 • 50
shuksi1984 • 50 wrote:
Following are my DNAseq pipeline steps keeping GATKBestPrac in mind:
Step1-Quality check of raw data (fastqc) Step2-Alignment with reference genome(bwa) Step3-SAM to BAM conversion and sorting (SortSam) step4-Generate aligment summary (CollectAlignmentSummaryMetrics, Samtools (depth), etc) step5-Duplicate marking (MarkDuplicates) Step6-Bam indexing (BuildBAMIndex) Step7-Perform local realignment (RealignerTargetCreator, IndelRealigner) Step8-Adjusting base quality score (BaseRecalibrator) Step-9-Recalibration run quality visualization (AnalyzeCovariates) Step10-Call Variants (HaplotypeCaller) Step11-Retain SNPs and Indels (SelectVatiants) Step12-Filter Indels and SNPs (VatiantFiltration) Step13-Filter reads based on various read properties (PrintReads) Step14-Detect additional variants (HaplotypeCaller) Step-15-Retain SNPs and Indels 2nd time (SelectVariants) Step16-Filter Indels and SNPs 2nd time (VatiantFiltration) Step17-Annotate SNPs (SnpEff) Step18-Generate genome coverage (bedtools)
I have mentioned the tools also. Kindly, let me know whether I am on track.
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