RFMIX is a program to identify the ancestry of genomic segments using random forest discriminative machine learning methods combined with a conditional random field model of the linear chromosome.

Web site

• Home page

• RFmix Documentation

• Module Name: rfmix (see the modules page for more information)

Allocate an interactive session and run the program.
Sample session (user input in bold):

[user@biowulf]$ sinteractive
salloc.exe: Pending job allocation 12345678
salloc.exe: job 12345678 queued and waiting for resources
salloc.exe: job 12345678 has been allocated resources
salloc.exe: Granted job allocation 12345678
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn1234 are ready for job

[user@cn1234 ~]$ module load rfmix

[user@cn1234 ~]$ rfmix --help
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

Summary of command line options - see manual for details

   -f , --query-file=	(required)
      VCF file with samples to analyze                      (required)
   -r , --reference-file=	(required)
      VCF file with reference individuals                   (required)
   -m , --sample-map=	(required)
      Reference panel sample population classification map  (required)
   -g , --genetic-map=	(required)
      Genetic map file                                      (required)
   -o , --output-basename=	(required)
      Basename (prefix) for output files                    (required)
   --chromosome=	(required)
      Execute only on specified chromosome                  (required)

   -c , --crf-spacing=
      Conditional Random Field spacing (# of SNPs)
   -s , --rf-window-size=
      Random forest window size (class estimation window size)
   -w , --crf-weight=
      Weight of observation term relative to transition term in conditional random field
   -G , --generations=
      Average number of generations since expected admixture
   -e , --em-iterations=
      Maximum number of EM iterations
   --reanalyze-reference
      In EM, analyze local ancestry of the reference panel and reclassify it

   -n , --node-size=
      Terminal node size for random forest trees
   -t , --trees=
      Number of tree in random forest to estimate population class probability
   --max-missing=
      Maximum proportion of missing data allowed to include a SNP
   -b , --bootstrap-mode=
      Specify random forest bootstrap mode as integer code (see manual)
   --rf-minimum-snps=
      With genetic sized rf windows, include at least this many SNPs regardless of span
   --analyze-range=
      Physical position range, specified as -, in Mbp (decimal allowed)

   --debug=
      Turn on any debugging output
   --n-threads=
      Force number of simultaneous thread for parallel execution
   --random-seed=
      Seed value for random number generation (integer)
	(maybe specified in hexadecimal by preceeding with 0x), or the string
	"clock" to seed with the current system time.

[user@cn1234 ~]$  vartrix --bam test_dna.bam --cell-barcodes dna_barcodes.tsv --fasta test_dna.fa --out-matrix test_dna.out --vcf test_dna.vcf

[user@cn1234 ~]$ exit
salloc.exe: Relinquishing job allocation 12345678
[user@biowulf ~]$

Create a batch input file (e.g. vartrix_job.sh). For example:

#!/bin/bash
set -e
module load vartrix
vartrix --bam test_dna.bam \
   --cell-barcodes dna_barcodes.tsv \
   --fasta test_dna.fa \
   --out-matrix test_dna.out \
   --vcf test_dna.vcf

Submit this job using the Slurm sbatch command.

sbatch [--cpus-per-task=#] [--mem=#] vartrix_job.sh

Create a swarmfile (e.g. vartrix_jobs.swarm). For example:

vartrix --bam test_dna1.bam \ 
   --cell-barcodes dna_barcodes1.tsv \
   --fasta test_dna1.fa \
   --out-matrix test_dna1.out \
   --vcf test_dna1.vcf
vartrix --bam test_dna2.bam \
   --cell-barcodes dna_barcodes2.tsv \
   --fasta test_dna2.fa \
   --out-matrix test_dna2.out \
   --vcf test_dna2.vcf
vartrix --bam test_dna3.bam \
   --cell-barcodes dna_barcodes3.tsv \
   --fasta test_dna3.fa \
   --out-matrix test_dna3.out \
   --vcf test_dna3.vcf

Submit this job using the swarm command.

swarm -f vartrix_jobs.swarm [-g #] [-t #] --module vartrix