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Old 11-28-2012, 11:59 PM   #1
whijae
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Location: Seoul

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Default RNA-Seq Variant Calling Softwares

I have searched for RNA-Seq variant calling programs and got a list of several programs. Could anyone suggest which program should be most reliable for cancer transcriptome data? (I meant RNA-Seq variant calling program without genome/exome data) Here is the list of programs I found.

SNVMix2
http://bioinformatics.oxfordjournals.../26/6/730.full

RNASEQR
http://nar.oxfordjournals.org/content/40/6/e42.long

SNVQ
http://www.biomedcentral.com/1471-2164/13/S2/S6

SNV-pipeline-v1.0
http://dir.nhlbi.nih.gov/papers/lmi/epigenomes/pma/

SAMtools mpileup -> bcftools
http://seqanswers.com/forums/showpos...00&postcount=1

VarScan
http://varscan.sourceforge.net/
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Old 11-29-2012, 12:59 AM   #2
syfo
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Interesting. I guess GATK is an option too.
You may want to take a look at this thread and this one.
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Old 12-07-2012, 12:35 PM   #3
dkoboldt
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A couple of cautions when doing variant calling using RNA-seq data:
1.) False positive rates are higher, both due to RT errors and the extra alignment difficulty of mapping mature mRNA transcripts to a reference genome. Look into Bowtie 2 and other packages that do this well, as the variant calling will only be as good as the alignment.

2.) Allelic expression bias may create some issues for Bayesian callers that expect alleles to be represented at 0%, 50%, or 100%. We use VarScan (a heuristic/statistic method) and specify lower minimum variant allele frequency to catch these (e.g. 0.08).

Good luck!

~Dan Koboldt
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