https://github.com/mfcovington/detect-boundaries
https://github.com/mfcovington/detect-boundaries
Last synced: over 1 year ago
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- Host: GitHub
- URL: https://github.com/mfcovington/detect-boundaries
- Owner: mfcovington
- Created: 2013-06-30T09:09:01.000Z (about 13 years ago)
- Default Branch: develop
- Last Pushed: 2016-02-17T05:13:12.000Z (over 10 years ago)
- Last Synced: 2025-02-14T15:15:33.400Z (over 1 year ago)
- Language: Perl
- Homepage:
- Size: 72.3 KB
- Stars: 1
- Watchers: 2
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
Awesome Lists containing this project
README
`merge-replicates.pl`: Use if there are multiple replicates for a single sample and the genotype files need to be merged.
- Input: Genotype files (one per chromosome per replicates for a sample)
- Output: Merged genotype files (one per chromosome)
`filter-snps.pl`:
- Input:
- Sample ID
- Genotype files (one per chromosome for a sample)
- Output:
- Boundaries file
- Filtered SNP files (one per chromosome)
### Notes:
detect-boundaries:`filter-snps.pl`
- IN:
- Genotyped files:
- OUT:
- Boundary files: `sample-file/RIL_300.boundaries`, etc.
- Filtered SNP files: `RIL_300.A01.filtered.snps`, etc.
### Merging Boundaries with `merge-boundaries.pl`
This script takes a collection of `*.boundaries` files and merges all of the boundaries. The bins resulting from the merge are written to a file: `bins.tsv`. Boundary and bin stats (count, min size, max size, and mean size) are printed to the screen.
Sample Usage:
```shell
./merge-boundaries.pl \
--bam_file ~/git.repos/sample-files/bam/IMB211.good.bam \
--chr_list A01,A02,A03,A04,A05,A06,A07,A08,A09,A10 \
sample-file/RIL_*.boundaries
```
- IN:
- Boundary files: `sample-file/RIL_300.boundaries`, etc.
- Representative `.bam` file (for extracting chromosome lengths)
- (Optional) Chromosome list (for limiting analysis to a subset of sequences)
- OUT:
- Comprehensive list of bins and their locations: `bins.tsv`
detect-boundaries:`extract-snp-subset.R`
- IN:
- VCF summaries: `/Users/mfc/git.repos/snps-from-rils/merged.EC50.minflter.vcf/summaries.het_ratio_0_1.alt_ratmin_0_05.filters/merged.*.EC50.minflter.vcf.summary`
- Bins: `bins.tsv`
- OUT:
- `sample-file/bins-snp.mid`
detect-boundaries:`get-genotypes-for-snp-subset.pl`
- IN:
- `sample-file/bins-snp.mid`
- Genotyped files:
- polyDB...
- list of Sample IDs
- OUT:
- `bin-genotype`
*Version 0.6.0*