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CAST-genomics / haptools

Ancestry and haplotype aware simulation of genotypes and phenotypes for complex trait analysis
https://haptools.readthedocs.io
MIT License
18 stars 4 forks source link

feat: Clump #211

Closed mlamkin7 closed 1 year ago

mlamkin7 commented 1 year ago

We've addded a new subcommand clump. Clump operates similar to Plink's --clump option except our version can accommodate tandem repeats such as STRs.

Example Usage: 

haptools clump \
  --summstats-snps tests/data/test_snpstats.linear \
  --gts-snps tests/data/simple.vcf \
  --clump-id-field ID \
  --clump-chrom-field CHROM \
  --clump-pos-field POS \
  --out test_snps.clump