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Polyploid support | PFR still trying to figure out how to analyze data PFR has no set format yet Current have VCF files Would like to store hyplotypes and polyploid genotypes Will GOBii be the main repository for VCF data???
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GOBii data storage solutions for polyploids/complex data types | Diploidize data Add new HDF5 datatype for tetraploids etc – PFR - for SNPs only for now A/A/A/T and A|A|A|T optional vcf for ps (phase set) integer for group specific for a dataset (but would want to use consistently across all datasets) . Ps not urgent. Padding HDF5 : AAAA and AA become AAAA and AA__ Look-up table : A / AAATA replaced ù / ĉ in HDF5, with translation back upon extract Try PostgreSQL 11: can handle variable length alleles Downstream analysis need read depth at diploid level, or dosage alleles A/T:15,6 or AAAT or T:0.25 or 0/0/0/1; 0.25, 0.25, 0.25, 0.25 Filtered markers – remove from file – already removed from the vcf during cleaning phase
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Student intern project: data management polyploids and indels | With simulated dataset 1250 samples, 0.5M markers, with mix of indels and ploidy Padded to largest indel Look up table for indels (and padding for ploidy) PostgreSQL 11 with partitioning, parallelization and indexing
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Questions | What is the genotyping data format of choice? Diploidized data – don’t want Nucleotides with dosage eg A/A/A/T - OK Maximum likelihood dosage eg GT:AD:GP 0/0/0/1:13,6:0.033,0.684,0.233,0.045,0.005 – not sure Haplotypes (1 row or multiple rows?) – multiple row easier ? Raw vcf; standard or variable formats? May still be variable – would need postgres solution then Geno call and vcf? Eg A/A/A/A; 0/0:3,0:3:88:0,9,108 – yes, Tim/Sue to send the best format Are there any mixed ploidy files (variable length) - No
Indels? Max size? Proportion? –5% and low confidence, 2-10 bp multiallelic What are the extract use-cases; cross ploidy, indels and SNPs, A/A/A/A and read depth format (Quality score too?)
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Lee’s travel to Cornell | GOBii hackathon is Sep 23, 2019 to Sep 27, 2019 . |