SNP detection (no reference) parameters
Hello,
I have sequenced the transcriptome of a non-model animal, including RNA from 4 different tissues of 10 individuals and normalizing.
I have performed the de novo assembly and mapping the reads to the contigs, now I have to do the SNP detection, but I do not know which parameters should I use for a successful in silico validation. Could anyone help me?
These are the parameters I can modify:
- number of gaps and mismatches (max ~ surrounding the polymorphic site) (2 is ok)
- surrounding bases mean quality score (I think 15 would be ok)
- site minimum quality (I think 20 is ok)
- minimum coverage
- minimum variant frequency (this can be replaced for: minimum variant count required __ and sufficient __; for example, if the count required is set to 1, and the sufficient count is set to 5, it means that even though less than the required percentage of the reads have a variant base, it will still be reported as a SNP if at least 5 reads have it).
Thank you in advance!!
I have sequenced the transcriptome of a non-model animal, including RNA from 4 different tissues of 10 individuals and normalizing.
I have performed the de novo assembly and mapping the reads to the contigs, now I have to do the SNP detection, but I do not know which parameters should I use for a successful in silico validation. Could anyone help me?
These are the parameters I can modify:
- number of gaps and mismatches (max ~ surrounding the polymorphic site) (2 is ok)
- surrounding bases mean quality score (I think 15 would be ok)
- site minimum quality (I think 20 is ok)
- minimum coverage
- minimum variant frequency (this can be replaced for: minimum variant count required __ and sufficient __; for example, if the count required is set to 1, and the sufficient count is set to 5, it means that even though less than the required percentage of the reads have a variant base, it will still be reported as a SNP if at least 5 reads have it).
Thank you in advance!!