Question: snp detection for RNA SEQ
0
gravatar for fatimarasool135
3.2 years ago by
fatimarasool13560 wrote:

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

rna-seq • 831 views
ADD COMMENTlink modified 3.2 years ago by Lila M 820 • written 3.2 years ago by fatimarasool13560

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

ADD REPLYlink written 3.2 years ago by cpad011214k
2
gravatar for WouterDeCoster
3.2 years ago by
Belgium
WouterDeCoster44k wrote:

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.

ADD COMMENTlink written 3.2 years ago by WouterDeCoster44k
0
gravatar for Lila M
3.2 years ago by
Lila M 820
UK
Lila M 820 wrote:

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

ADD COMMENTlink written 3.2 years ago by Lila M 820
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