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keller_and_evans_lab:gscan [2016/04/27 16:33] scott /* Coordination and organization */ |
keller_and_evans_lab:gscan [2016/09/12 14:57] scott /* Phenotype definitions and analysis plan */ |
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Regular conference calls are held and minutes are [[https:// | Regular conference calls are held and minutes are [[https:// | ||
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+ | Other meeting materials from CO internal meetings are here: | ||
+ | |||
+ | [[gscan_6: | ||
======= GSCAN Exome Chip ======= | ======= GSCAN Exome Chip ======= | ||
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+ | |||
+ | ====== Phenotype definitions and analysis plan ====== | ||
+ | |||
+ | {{file_gscan_exome_chip_analysis_plan-v2_2.pdfExome chip analysis plan and phenotype definitions.}} | ||
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======= GSCAN GWAS ======= | ======= GSCAN GWAS ======= | ||
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+ | |||
+ | ====== Phenotype definitions and analysis plan ====== | ||
+ | |||
+ | The analysis plan and phenotypes are described in files linked below (makes it easier to keep track of versioning!). Coding of phenotypes is described in the aptly-named " | ||
+ | |||
+ | {{file_gscan_gwas_analysis_plan-v1_3.docxClick here to find the GSCAN GWAS analysis plan.}} | ||
+ | |||
+ | {{file_gscan_gwas_phenotype_definitions-2-24-2016.pdfClick here to find the GSCAN GWAS phenotype definitions.}} | ||
====== Coordination and organization ====== | ====== Coordination and organization ====== | ||
- | Progress, internal and external, are tracked in [[https:// | + | Progress, internal and external, are tracked in [[https:// |
Study contact info is tracked in [[https:// | Study contact info is tracked in [[https:// | ||
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On RC the organization is similar. Everything is located within the folder / | On RC the organization is similar. Everything is located within the folder / | ||
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+ | |||
+ | ====== [[gscan_db_ga_p]] ====== | ||
+ | |||
+ | Studies included from dbGaP, and the process by which phenotypes and genotypes were constructed and merged is outlined on the [[gscan_db_ga_p]] page. | ||
+ | |||
+ | |||
+ | ====== GSCAN use of UKBiobank ====== | ||
+ | |||
+ | More information about the files used for [[uk_biobank|UKBiobank are here]]. In brief, we used the UK10K + 1kgp3 imputed vcfs provided by UKBionank and added in dosages w/ this python script: | ||
+ | |||
+ | import gzip, argparse, re, os, datetime | ||
+ | from subprocess import Popen, PIPE | ||
+ | |||
+ | def add_dosage(pair): | ||
+ | a, b = pair | ||
+ | probs = b.split(b',' | ||
+ | dose = float(probs[1]) + (float(probs[2]) * 2) | ||
+ | return a + b':' | ||
+ | |||
+ | def gziplines(fname): | ||
+ | f = Popen([' | ||
+ | for line in f.stdout: | ||
+ | yield line | ||
+ | |||
+ | parser = argparse.ArgumentParser() | ||
+ | parser.add_argument(' | ||
+ | args = parser.parse_args() | ||
+ | |||
+ | flag = False | ||
+ | |||
+ | for line in gziplines(args.inputVCF): | ||
+ | if line.startswith(b'#' | ||
+ | os.write(1, line.rstrip() + b' | ||
+ | if not flag: | ||
+ | os.write(1, b'## | ||
+ | os.write(1, b'## | ||
+ | str(datetime.datetime.now()).encode(' | ||
+ | flag = True | ||
+ | else: | ||
+ | elements = re.split(b' | ||
+ | first8 = elements[: | ||
+ | genotypes = elements[10: | ||
+ | form = b' | ||
+ | |||
+ | genotypes_split = zip(genotypes[:: | ||
+ | try: | ||
+ | dose_genos = [add_dosage(pair) for pair in genotypes_split] | ||
+ | except (ValueError, | ||
+ | os.write(2, " | ||
+ | os.write(2, line + " | ||
+ | raise e | ||
+ | os.write(1, b' | ||
+ | |||
======= GSCAN Sequencing ======= | ======= GSCAN Sequencing ======= | ||
+ | |||
+ | |||
+ | ====== TOPMed ====== | ||
+ | |||
+ | |||
+ | ===== Phenotype definitions and analysis plan ===== | ||
+ | |||
+ | Phenotype definitions and analysis plans for the TOPMed studies are {{file_topmed_smoking_analysis_plan-v0_2_281_29.docx_contained_in_this_document}}. | ||
The list of dbGaP studies in TOPMed is in [[https:// | The list of dbGaP studies in TOPMed is in [[https:// | ||
+ |