Question: Multiple RNAseq Library to SNP Call using GATK
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gravatar for Bioinfonext
24 months ago by
Bioinfonext140
Korea
Bioinfonext140 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 SJ.out.tab 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 • 796 views
ADD COMMENTlink modified 18 months ago by Biostar ♦♦ 20 • written 24 months ago by Bioinfonext140

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 24 months ago • written 24 months ago by WouterDeCoster38k
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