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filtering variants for non human before performing BQSR

mayaabmayaab IsraelMember ✭✭

Hello,
I would like to call variants on non human genome (S.Cerevisiae).
I understood that I should perform These steps:
1. Indel realignment
2. HC to have SNPs data base
3. variant filtration to get the more confident variants
4. running BQSR with the vriants as data base.
5. running HC on the BQSR data

my questions are:
How should I perform the filtration of the variants in 3? do you have any recommendations?
I would like to find variants only for one sample. should I use more samples for creating the variant data base, or one sample can be enough (I have 7 samples of that project, and I can use them)?

Maya

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