snp detection for RNA SEQ

Question

[fatimarasool135]

what is the best tools for SNP detection for RNA SEQ data?and how to convert bam.bai files into bam file?

[cpad0112]

an example GATK best practices workflow for variant calling in RNAseq data, using bpipe: https://digibio.blogspot.in/2015/07/variant-calling-in-rna-seq-and-bpipe.html

Answer 1

[WouterDeCoster]

what is the best tools for SNP detection for RNA SEQ data?

Have a look at GATK Best Practices for variant calling on RNAseq

and how to convert bam.bai files into bam file?

You can't. A .bai file is an index of a bam file and doesn't contain the same information.

Answer 2

[Lila M]

You can also have a look to other post with lot of information as Workflow Or Tutorial For Snp Calling?