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README.md
extract-snp-subset.R
extract-snp-subset.pl
filter-snps.pl
find-genotype-y-bins-similar-to-genotype-x-bins.pl
find-similar-bins.pl
fine-tune-boundaries.pl
get-genotypes-for-bins.pl
get-genotypes-for-snp-subset.pl
impute-NAs-at-chromosome-ends.pl
merge-boundaries.pl
merge-replicates.pl
plot-bin-stats.R
plot-composite-map.R
plot-filtered-snps.R

README.md

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:

./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