Tagged with #snps
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Hi! I have worked some time on a mRNAseq set, single-end. Its a high quality set and lots of biological replicates (200+).

My question is, how could I best contribute to the methodology used for SNPs call in mRNAseq? What do we need tested to improve this method?

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For exome-sequencing, I was wondering how I should decide the "-mode" parameter? should I use "SNP" or "Indel" or both? I want to get both information in the final results, should I use "BOTH" -mode?

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I was wondering, in the vcf output from UnifiedGenotyper what metrics go into the variant quality score, QUAL ?

I'm assuming that depth, DP is one of them but I can't find further information. Apologies if I've missed it.

Attached are some plots of the depth and quality distribution for variant calls, and also of the relationship between depth and quality. I'm slightly worried that the bimodal quality distribution indicates an error, otherwise I've just attached the graphs for general interest.

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I have used UnifiedGenotyper to call SNPS. I found some SNPs that has been reported from low quality reads in chromosome X and chromosome Y. Is it possible not to take low quality reads into account while calling SNPs using UnifiedGenotyper? Or, do I need to do quality filtering of BAM files before hand ?