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Which Snp Caller / Method To Use After Aligning Rna-Seq With Tophat

Which SNP caller / method can / should I use after aligning RNA-seq data with TopHat?

For genomic data I use GATK, but supposedly it is not just as easy as running GATK on the TopHat RNA-seq data. The team from Broad has no information / documentation on how to use GATK for RNA-seq data.

I don't have any variants yet from DNA re-sequencing.

snp tophat2 rna-seq
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updated by jockbanan jockbanan • written by William William

3 answers

VarScan will happily make calls on RNAseq data with a matched normal (from RNAseq or exome). Be sure to consider all of the parameters carefully, especially minimum coverage levels and such.

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written by Chris Miller Chris Miller

Do you have some advices for strand-specific RNA-Seq (2x50bp) ?

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written by Nicolas Rosewick Nicolas Rosewick

Don't have a lot of experience with this, but some tools have steps with a directional filter (variants only appearing in one strand are removed as artifacts). Make sure that any such option is off.

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written by Chris Miller Chris Miller

I haven't looked at GATK on RNA-seq data, instead I used samtools/BCFtools, it's probably not the best, but it will get you started.

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written by yyaobo • yyaobo

Current GATK (2.8-1) seems not to be a good option for reads mapped with TopHat (and any other splice-aware aligners). When running on .bam file generated by TopHat, you end up with an error saying you should remove (or ignore) all reads with 'N' cigar string (spliced reads). You can force GATK to process these reads, but the authors say that this may result in something not really meaningful.

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written by jockbanan jockbanan

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