Question: Multiple RNAseq Library to SNP Call using GATK
gravatar for Bioinfonext
2.9 years ago by
Bioinfonext200 wrote:

1) I want to run star 2 pass pipeline: After running 1-star mapping, I got SJ.OUT.TAB for each library , now please suggest after concatenate all the files into one file, how to perform the filtering, and use only this filtered file.

2) ) Is it required to do Indel Realignment and base Recalibration while calling SNP from RNAseq data?

3) ) Which variant caller should I used, if I have multiple bam files. do I use Haplotype caller or GenotypeGVCFs by merging all bam file?

I will be thankful to you for helping me.

snp • 1.1k views
ADD COMMENTlink modified 2.4 years ago by Biostar ♦♦ 20 • written 2.9 years ago by Bioinfonext200

Maybe it's time to start reading manuals of tools, and follow guidelines, or figure things out on your own. You are learning absolutely nothing by making a new question for every single step in your analysis. Doing bioinformatics and learning new things takes time. If you have been stuck for days it's okay to ask for help, but a correct attitude would be to try more stuff on your own.

ADD REPLYlink modified 2.9 years ago • written 2.9 years ago by WouterDeCoster43k
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