Hello,
I just received SOLiD 75bp fragment (SE) exome data. I haven't previosly worked with SOLiD data and I'm not sure the suitable way to handle them for a further GATK based variant detection. In concrete I have doubts about:
- filtering PCR duplicated
I'm undecided to filter or not them using picard markduplicates. Being SingleEnd data I'm inclined not to do it to avoid lose "true" reads (not duplicates) at expense of generate "dirty" variant calls. What's you opinion?.
- base recalibration
Due to special caracteristics of colorspace read seems to be unnecessary to make base recalibration. I checked "1000 Genomes" paper (http://www.nature.com/nature/journal...ture09534.html) where based recalibration was avoided for SOLiD data. By other hand, in GATK documentation (http://www.broadinstitute.org/gsa/wi..._recalibration) "PrimerRoundCovariate" covariate is described as "The primer round for this base (only meaningful for SOLiD reads).". I'm confused and do not know if the recalibration of bases is a recommended step for SOLiD.
Any advice?
I would appreciate your help.
Thank you
I just received SOLiD 75bp fragment (SE) exome data. I haven't previosly worked with SOLiD data and I'm not sure the suitable way to handle them for a further GATK based variant detection. In concrete I have doubts about:
- filtering PCR duplicated
I'm undecided to filter or not them using picard markduplicates. Being SingleEnd data I'm inclined not to do it to avoid lose "true" reads (not duplicates) at expense of generate "dirty" variant calls. What's you opinion?.
- base recalibration
Due to special caracteristics of colorspace read seems to be unnecessary to make base recalibration. I checked "1000 Genomes" paper (http://www.nature.com/nature/journal...ture09534.html) where based recalibration was avoided for SOLiD data. By other hand, in GATK documentation (http://www.broadinstitute.org/gsa/wi..._recalibration) "PrimerRoundCovariate" covariate is described as "The primer round for this base (only meaningful for SOLiD reads).". I'm confused and do not know if the recalibration of bases is a recommended step for SOLiD.
Any advice?
I would appreciate your help.
Thank you
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