Version 1.0: 12.22.17
This suite of modules is meant to ease the babysitting load for routinely processing genotype files to ADMIXTURE or imputation.
- Requires Python 3.6.3, but will identify Python version and update if needed.
- Starts from plink bed/bim/fam files. I'll eventually add other file formats.
Always start using python genoprocess.py then you will see a screen asking you what you'd like to do next.
Sees what version of Python you're running.
Downloads Python 3.6.3 if you're on linux and exits telling you to download it if on Mac or Windows.
Asks the user if they would like to do the following:
| genoprocess task | Short description | System requirements | Notes |
|---|---|---|---|
| 1 | Download reference files and programs | Most any, some Mac or Linux | Some programs will not download if you aren't on Linux because they are Linux based |
| 2 | Update sex | Any | |
| 3 | Produce new dataset of people and SNPs with missince all rate < 10% | Any | |
| 4 | Run IBD matrix through Plink | Any | |
| 5 | Update family (FID) and individual IDs (IID) | Any | |
| 6 | Update maternal and paternal IDs | Any | |
| 7 | Harmonize with 1000G Phase 3 | Any | |
| 8 | Filter for extreme (+-3SD) heterozygosity values | Any | |
| 9 | Merge with 1000G Phase 3 | Any | |
| 10 | Prepare for ADMIXTURE with k = 3...9 | Mac or Linux | I will submit the job for you if you're on the Penn State ACI-B cluster |
| 11 | Run a phasing check and prepare files for phasing using SHAPEIT 2 | Mac or Linux | I will submit the job for you if you're on the Penn State ACI-B cluster |
| 12 | Prepares files for imputation using the Sanger Imputation Server | Mac or Linux | |
| 13 | Nothing |
Downloads the following:
- Python 3.6.3
- Plink 1.9
- 1000G Phase 3 VCF
- 1000G Phase 3 Hap/Legend/Sample
- GRCh37/hg19 1000G FASTA file
- Genotype Harmonizer
- pip
- snpflip
- shapeit
- vcftools
- bcftools
- htslib
- samtools
Update sex
Missing call rate
Heterozygosity check
Run IBD to identify relatives
Update FID & IID information
Update parental IDs
Harmonize with 1000G
Merge with 1000G
Prepare for admixture, submit job if on Penn Sate ACI-B cluster
| Should be done before admixture | genoprocess number | Module used |
|---|---|---|
| Keep only SNPs and people with missing call rate < 10% | #3 | genoqc.missing_call_rate() |
| Run IBD to identify relatives | #4 | genorelatives.ibd() |
| Update FID and/or IID information | #5 | genorelatives.update_id() |
| Update parental IDs | #6 | genorelatives.update_parental() |
| Harmonize with 1000G Phase3 | #7 | genoharmonize.harmonize_with_1oooG() |
| Filter out individuals with extreme heterozygosity values | #8 | genoqc.het() |
| Merge with 1000G | #9 | genomerge.merge1000g() |
Checks data and prepares for phasing using shapeit.
Checks phased data for imputation
| Should be done before phasing | genoprocess number | Module used |
|---|---|---|
| Genotypes must be on GRCh37/hg19 | User should check this | None |
| Keep only SNPs and people with missing call rate < 10% | #3 | genoqc.missing_call_rate() |
| Filter out individuals with extreme heterozygosity values | #8 | genoqc.het() |
| Filter out SNPs with MAF < 5% | #7 | genoharmonize.harmonize_with_1000G() |
| Filter out SNPs with HWE p-value < 0.05 | #7 | genoharmonize.harmonize_with_1000G() |
| Set haploid genotypes (male ChrX) as missing | User should check this if any warnings of het haploid genotypes appear | None |
| Check for gender mismatches | #2 | genoqc.update_sex() |
| Harmonize with 1000G Phase3 | #7 | genoharmonize.harmonize_with_1000G() |