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March 17, 2021 00:07
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SHAPEIT4 error for chromosome X: "ERROR: No variants to be phased"
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| SHAPEIT | |
| * Author : Olivier DELANEAU, University of Lausanne | |
| * Contact : olivier.delaneau@gmail.com | |
| * Version : 4.1.2 | |
| * Run date : 16/03/2021 - 18:28:17 | |
| Files: | |
| * Input VCF : [cohort-chrX.release.vcf.gz] | |
| * Genetic Map : [chrX.b38.gmap.gz] | |
| * Output VCF : [cohort-chrX.release.phased.vcf.gz] | |
| * Output LOG : [shapeit4_output_dvglx_chrX.txt] | |
| Parameters: | |
| * Seed : 15052011 | |
| * Threads : 12 threads | |
| * MCMC : 15 iterations [5b + 1p + 1b + 1p + 1b + 1p + 5m] | |
| * PBWT : Depth of PBWT neighbours to condition on: 4 | |
| * PBWT : Store indexes at variants [MAC>=2 / MDR<=0.5 / Dist=0.0005 cM] | |
| * HMM : K is variable / min W is 2.50cM / Ne is 15000 | |
| * HMM : Recombination rates given by genetic map | |
| * HMM : AVX2 optimization active | |
| * IBD2 : length>=3.00cM [N>=10000 / MAF>=0.000 / MDR<=0.500] | |
| Initialization: | |
| ERROR: No variants to be phased in [cohort-chrX.release.vcf.gz] |
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