Varscan for snp detection instead of gatk

[madsaan]

Hi,

I am trying to detect snp's in a pooled sample of total RNA.I understand that GATK is a very popular tool for variant detection ,SNP & Indel discovery.I would like to know if it is possible to use GATK for pooled RNA samples that have been aligned with reference genome?If yes, is varscan better than GATK?

Thanks,
Joji

[Jose Blanca]

GATK is a good tool, but for certain analysis we needed something different so, we programmed our own little tool. Take it a look, it might give you some ideas.

http://bioinf.comav.upv.es/ngs_backbone/

[dkoboldt]

SNP detection: VarScan or GATK

Dear Joji,

I've not done a direct comparison, but certainly VarScan is designed to allow variant detection in pooled samples. RNA data adds another complication, as alleles may not be equally represented.

My experience with GATK is limited to the IndelGenotyper, which is pretty good - highly specific, perhaps at a slight cost of sensitivity.

Yours,

Dan

Hi,

I am trying to detect snp's in a pooled sample of total RNA.I understand that GATK is a very popular tool for variant detection ,SNP & Indel discovery.I would like to know if it is possible to use GATK for pooled RNA samples that have been aligned with reference genome?If yes, is varscan better than GATK?

Thanks,
Joji

[ozs2006]

Hi,

Does anyone know why varScan detects two variants in the same genomic position, same variation but different quality scores?

example:
chr1 557915 T Y 140 13 8.5% 2 2 30 32 0.98 1 1 39 101 2 11 C
chr1 557915 T K 140 13 8.5% 2 2 30 30 0.98 1 1 39 101 2 11 C

or

chr1 555884 A G 9 753 98.82% 2 2 30 31 0.98 1 1 3 6 14 739 G
chr1 555884 A W 9 6 40% 2 2 30 32 0.98 1 1 3 6 3 3 G

Thanks in advance,
Oz