Next Generation Sequencing Of Pooled Samples: Guideline For Variants’ Filtering Samples Guide
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- Next Generation Sequencing of Pooled Samples: Guideline for Variants’ Filtering
- Results and Discussion
- Sequencing results.
- Variant Call.
- Public database annotations.
- Comparison with 1000genomes and ExAC.
- Validation of Pool-seq AF: comparison with Immunochip SNP-array.
- Sequencing errors and rare alleles.
- Filtering guideline using Kolmogorov-Smirnov (KS) test: Quality Filter (QF).
- Minimum Percentage of reads Filter (MPF) as an alternative filter.
- Getting the best out of two filters.
- Validation of filters.
- Possible applications of filtering guideline.
- Conclusions
- Methods
- Pooling and sequencing of target-regions.
- Bioinformatic pipeline.
- Variant call using CRISP and variant annotations.
- Comparison with Immunochip SNP-array.
- AF calculation and AF with MPF filter.
- Kolmogorov-Smirnov (KS) test.
- Comparison with individual sequencing variants of one of the pools.
- Analysis tools.
- Acknowledgements
- Author Contributions
- Figure 1. (a) Allele Frequency distribution of all variants.
- Figure 2. Comparison of poolAF with AF of 1000genomes.
- Figure 3. Pool sequencing AF vs.
- Figure 4. QUAL(ity) score distribution of all variants.
- Figure 5. Density distributions of QUAL(ity) scores of variants found in public databases (in.
- Table 1. Summary of comparison of Pool-seq variants with variants obtained from individual sequencing of the same pool (before and after filtering).
- Results and Discussion