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In most cases, it is expected that all samples will be collected and phenotyped before applying for the NIH CIDR Program. Possible exceptions should be discussed with CIDR and the NIH supporting institute before applying.
Next Generation Sequencing Platform
Illumina HiSeq sequencers
Indexed, 100 bp, paired end runs
||5ug of genomic DNA
||DNA should be sent in 1XTE, pH 8.0 (10mMTris, 1mM EDTA). Do not use water
||Blood, cell line or saliva
||Please inquire about other DNA sources
- Sample pretesting with a high density SNP array
- This allows us to:
- Determine SNP genotypes for sample tracking and sequencing variant call QC purposes
- Identify file and/or aliquoting errors (primarily gender and/or Mendel discrepancies)
- Identify unexpected relatives among subjects, confirm expected relationships
- Identify samples that perform poorly
- Identify unexpected duplicate samples, confirm expected relationships
- Data will be generated to an average of 30x coverage
- Data will be generated to a minimum high density SNP array concordance of >99%.
- SNVs and indels called and annotated
- Data quality evaluated using a robust alignment and variant calling workflow implemented via CIDRSeqSuite in-house pipeline. Any of the files detailed in the analysis workflow will be available for distribution to the PI. Image and intensity level data is not retained.
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