Multiple RNAseq Library to SNP Call using GATK
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.
• 2,068 views
•
link
updated
by
Biostar
•
written
by
Bioinfonext
•
written
by
Bioinfonext
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
GATK - Output differences in Calls when Split by chromosome intervals and without splitting
written by Maverick •
-
STAR: Two-Pass mapping, Should SJ.out.tab files be filtered out or not?
written by conor93
-
Using STAR SJ.out.tab file to identify novel ncRNAs
written by jennifer.conrad84 •
-
How to create SJ.out.tab files from bam files
written by freeustand •
-
STAR-Fusion empty result
written by MatthewP
-
STAR mapping pipeline with 2-pass for multiple samples?
written by Rajesh Detroja
-
GATK; Variant calling RNA-Seq best practices: bam processing steps
written by user230613
-
Query related to SNP calling from RNAseq data using GATK
written by Bioinfonext
-
STAR-2 PASS raw read mapping for SNP calling using GATK
written by Bioinfonext
-
IndelRealigner and RealignerTargetCreator for amplicon sequencing
written by kulvait
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.