Generic genetic map

[rodrigopsav]

Hello, I've been working with LPS imputation and I am trying to use a generic genetic map. I've got the following message. Is there any suggestion how to write a generic genetic map of 1cMperMb? Thanks

$(dirname $CONDA_PREFIX)/imputeme/bin/QUILT_prepare_reference.R \

--chr=$CHR
--regionStart=2000000
--regionEnd=3000000
--buffer=200000
--reference_haplotype_file=impute_onlyHol_woHolSra_chr29.hap.gz
--reference_legend_file=impute_onlyHol_woHolSra_chr29.legend.gz
--outputdir=quilt_output
--genetic_map_file=genMap_1cMperMb_29.txt
--tempdir=tmp
--nGen=100
Warning message:
package ‘optparse’ was built under R version 4.0.5
Warning message:
package ‘QUILT’ was built under R version 4.0.5
[2021-07-21 13:19:02] Running QUILT_prepare_reference(outputdir = quilt_output, chr = 29, nGen = 100, regionStart = 2000000, regionEnd = 3000000, buffer = 200000, output_file = , reference_haplotype_file = impute_onlyHol_woHolSra_chr29.hap.gz, reference_legend_file = impute_onlyHol_woHolSra_chr29.legend.gz, reference_sample_file = , reference_populations = NA, reference_phred = 30, reference_exclude_samplelist_file = , region_exclude_file = , genetic_map_file = genMap_1cMperMb_29.txt, nMaxDH = NA, tempdir = tmp, make_fake_vcf_with_sites_list = FALSE, output_sites_filename = NA, expRate = 1, maxRate = 100, minRate = 0.1)
[2021-07-21 13:19:02] Program start
[2021-07-21 13:19:02] Begin converting reference haplotypes
[2021-07-21 13:19:03] Begin get haplotypes from reference
[2021-07-21 13:19:03] Load and validate reference legend header
[2021-07-21 13:19:03] Load and validate reference legend
[2021-07-21 13:19:03] Extract reference haplotypes
[2021-07-21 13:19:03] In the region to be imputed plus buffer there are the following number of SNPs:
[2021-07-21 13:19:03] 11868 from the posfile
[2021-07-21 13:19:03] 11868 from the reference haplotypes
[2021-07-21 13:19:03] 11868 in the intersection of the posfile and the reference haplotypes
[2021-07-21 13:19:05] Succesfully extracted 1996 haplotypes from reference data
[2021-07-21 13:19:05] End get haplotypes from reference
[2021-07-21 13:19:05] Getting and validating genetic map
position COMBINED_rate.cM.Mb. Genetic_Map.cM.
1 2000090 1 2.000090
2 2000144 1 2.000144
Error in validate_genetic_map(genetic_map) :
Error interpreting genetic map around row 1. Provided genetic map does not satisfy expectations. See above print. Let g be the genetic map with 3 columns. In 1-based coordinates, recall that g[iRow, 3] must equal g[iRow - 1, 3] + ( (g[iRow, 1] - g[iRow - 1, 1]) * g[iRow - 1, 2])
Calls: QUILT_prepare_reference ... get_and_validate_genetic_map -> validate_genetic_map
Execution halted

[rwdavies]

Ah, so QUILT can work without a reference panel (see below the help message for the genetic map file option). In that case, it should default to 1 cM/Mbp (the default of expRate)

Path to file with genetic map information, a file with 3 white-space delimited entries giving position (1-based), genetic rate map in cM/Mbp, and genetic map in cM. If no file included, rate is based on physical distance and expected rate (expRate) [default \"\"]

[rodrigopsav]

Thanks for your help.

[PMuchina]

@rwdavies in your response did you mean QUILT can work without a genetic map? assuming a recombination rate of 1 cM/Mbp.

[rwdavies]

Yes it should work, with expRate setting the default, I'm not sure about all combinations, but I just checked the simplest acceptance test in QUILT/tests/testthat/test-acceptance-one.R and deleted the genetic map input to QUILT_prepare_reference and it ran

[PMuchina]

Yes, it worked for me to. Thank you