Question: DNAseq pipeline steps
1
gravatar for shuksi1984
23 months ago by
shuksi198450
shuksi198450 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.

alignment next-gen • 1.2k views
ADD COMMENTlink written 23 months ago by shuksi198450

You should perhaps mention what you aim to achieve.

ADD REPLYlink written 23 months ago by WouterDeCoster43k

I want to find out SNPs and indels.

ADD REPLYlink written 23 months ago by shuksi198450

If you want to use the 'best practices', according to the GATK, then just follow their most updated pipeline that is on their website. Have you done NGS data processing in the past?

ADD REPLYlink written 23 months ago by Kevin Blighe60k

No, I havent done. This is the 1st time I am doing.

just follow their most updated pipeline that is on their website

Can you share the link?

ADD REPLYlink written 23 months ago by shuksi198450

I am very new in WGS, WES analysis. I was wondering if this workflow that you mentioned worked for you?

ADD REPLYlink written 14 months ago by maria2019100
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 889 users visited in the last hour