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slowkoni / rfmix

RFMIX - Local Ancestry and Admixture Inference Version 2
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STOP: genetic map for chromosome is not strictly increasing. #16

Closed rozaimirazali closed 5 years ago

rozaimirazali commented 5 years ago

RFMIX v2.03-r0 - Local Ancestry and Admixture Inference (c) 2016, 2017 Mark Koni Hamilton Wright Bustamante Lab - Stanford University School of Medicine Based on concepts developed in RFMIX v1 by Brian Keith Maples, et al.

This version is licensed for non-commercial academic research use only For commercial licensing, please contact cdbadmin@stanford.edu

--- For use in scientific publications please cite original publication --- Brian Maples, Simon Gravel, Eimear E. Kenny, and Carlos D. Bustamante (2013). RFMix: A Discriminative Modeling Approach for Rapid and Robust Local-Ancestry Inference. Am. J. Hum. Genet. 93, 278-288

Loading genetic map for chromosome 22 ...
STOP: genetic map for chromosome 22 is not strictly increasing.

Anybody encountered this problem before?

rozaimirazali commented 5 years ago

This is my command:

rfmix --query-file=chr22.q.phased.vcf.gz --reference-file=chr22.1kg.phased.vcf.gz --sample-map=subpop_id.txt --genetic-map=genetic_map_hg19_withX.txt --output-basename=result --chromosome=22

rozaimirazali commented 5 years ago

The genetic map file that I downloaded from the Eagle website actually contains 4 columns

chr | position | COMBINED_rate(cM/Mb) | Genetic_Map(cM)

Just take 1st, 2nd and 4th column and write to a new file and use the new file as the genetic map.