[GLIMPSE2] Phase and impute low coverage sequencing data * Authors : Simone RUBINACCI & Olivier DELANEAU, University of Lausanne * Contact : simone.rubinacci@unil.ch & olivier.delaneau@unil.ch * Version : GLIMPSE2_phase v2.0.0 / commit = 3bed6d9 / release = 2022-12-07 * Citation : BiorXiv, (2022). DOI: https://doi.org/10.1101/2022.11.28.518213 * : Nature Genetics 53, 120–126 (2021). DOI: https://doi.org/10.1038/s41588-020-00756-0 * Run date : 24/01/2024 - 17:09:41 Files: * Input BAM/CRAM : [offspring/5X/5X_s18_sorted_chr17.bam] * Reference VCF : [BCFtools_Oni17_HD_Parents_pos_newinfo.bcf] * Genetic Map : [chr17.gmap] * Output file : [GLIMPSE_impute/s18_imputed_LG17_1_8486843.bcf] * Output format : [BCF format | ZLIB compression] GLIMPSE_phase parameters: * Imputation model : [Reference panel imputation] * Input region : [LG17:1-8486843] * Output region : [LG17:1-7486843] * Sparse MAF : [0.001] * Recombination rates : [Given by genetic map] * Ploidy : [Only diploid samples in region] * Keep monom. ref sites: [NO] Model parameters: * #Burnin iterations : [5] * #Main iterations : [15] * Ne [eff. pop. size] : [100000] * Phase error rate : [0.0001] * Imputation error rate: [1e-12] * Min value for hap GLs: [1e-10] Selection parameters: * K init : [1000] * K pbwt : [2000] * PBWT depth : [12] * PBWT modulo (cM) : [0.1] * State list : [No list provided] Genotype calling: * Calling model : [standard] * Perform calling] BAM/CRAM filters and options: * Min mapping quality : [10] * Min base quality : [10] * Max depth : [40] * Keep failed QC : [NO] * Keep orphan reads : [NO] * Keep duplicate reads : [NO] * Keep supp. alignment : [NO] * Check pairing : [NO] * Ignore orientation : [NO] * Illumina-1.3+ : [NO] Other parameters * Seed : [15052011] * #Threads : [1] Initialisation: Parsing specified genomic regions * Input region [LG17:1-8486843] * Output region [LG17:1-7486843] * VCF/BCF scanning ... * VCF/BCF scanning [L=41739 (Lrare= 0 (0.0%) - Lcommon= 41739 (100.0%))] * VCF/BCF scanning [Nm=1 (Nmh=0 - Nmd=1) / Nr=126 (Nrh=0 - Nrd=126)] * VCF/BCF scanning [Reg=LG17:1-8486843 / L=41739] [0.00s] * Reference panel parsing ... ERROR: AC/AN INFO fields in VCF are inconsistent with GT field, update the values in the VCF [GLIMPSE2] Phase and impute low coverage sequencing data * Authors : Simone RUBINACCI & Olivier DELANEAU, University of Lausanne * Contact : simone.rubinacci@unil.ch & olivier.delaneau@unil.ch * Version : GLIMPSE2_phase v2.0.0 / commit = 3bed6d9 / release = 2022-12-07 * Citation : BiorXiv, (2022). DOI: https://doi.org/10.1101/2022.11.28.518213 * : Nature Genetics 53, 120–126 (2021). DOI: https://doi.org/10.1038/s41588-020-00756-0 * Run date : 24/01/2024 - 17:09:41 Files: * Input BAM/CRAM : [offspring/5X/5X_s18_sorted_chr17.bam] * Reference VCF : [BCFtools_Oni17_HD_Parents_pos_newinfo.bcf] * Genetic Map : [chr17.gmap] * Output file : [GLIMPSE_impute/s18_imputed_LG17_6486833_12486914.bcf] * Output format : [BCF format | ZLIB compression] GLIMPSE_phase parameters: * Imputation model : [Reference panel imputation] * Input region : [LG17:6486833-12486914] * Output region : [LG17:7486850-11486910] * Sparse MAF : [0.001] * Recombination rates : [Given by genetic map] * Ploidy : [Only diploid samples in region] * Keep monom. ref sites: [NO] Model parameters: * #Burnin iterations : [5] * #Main iterations : [15] * Ne [eff. pop. size] : [100000] * Phase error rate : [0.0001] * Imputation error rate: [1e-12] * Min value for hap GLs: [1e-10] Selection parameters: * K init : [1000] * K pbwt : [2000] * PBWT depth : [12] * PBWT modulo (cM) : [0.1] * State list : [No list provided] Genotype calling: * Calling model : [standard] * Perform calling] BAM/CRAM filters and options: * Min mapping quality : [10] * Min base quality : [10] * Max depth : [40] * Keep failed QC : [NO] * Keep orphan reads : [NO] * Keep duplicate reads : [NO] * Keep supp. alignment : [NO] * Check pairing : [NO] * Ignore orientation : [NO] * Illumina-1.3+ : [NO] Other parameters * Seed : [15052011] * #Threads : [1] Initialisation: Parsing specified genomic regions * Input region [LG17:6486833-12486914] * Output region [LG17:7486850-11486910] * VCF/BCF scanning ... * VCF/BCF scanning [L=56443 (Lrare= 0 (0.0%) - Lcommon= 56443 (100.0%))] * VCF/BCF scanning [Nm=1 (Nmh=0 - Nmd=1) / Nr=126 (Nrh=0 - Nrd=126)] * VCF/BCF scanning [Reg=LG17:6486833-12486914 / L=56443] [0.00s] * Reference panel parsing ... ERROR: AC/AN INFO fields in VCF are inconsistent with GT field, update the values in the VCF [GLIMPSE2] Phase and impute low coverage sequencing data * Authors : Simone RUBINACCI & Olivier DELANEAU, University of Lausanne * Contact : simone.rubinacci@unil.ch & olivier.delaneau@unil.ch * Version : GLIMPSE2_phase v2.0.0 / commit = 3bed6d9 / release = 2022-12-07 * Citation : BiorXiv, (2022). DOI: https://doi.org/10.1101/2022.11.28.518213 * : Nature Genetics 53, 120–126 (2021). DOI: https://doi.org/10.1038/s41588-020-00756-0 * Run date : 24/01/2024 - 17:09:41 Files: * Input BAM/CRAM : [offspring/5X/5X_s18_sorted_chr17.bam] * Reference VCF : [BCFtools_Oni17_HD_Parents_pos_newinfo.bcf] * Genetic Map : [chr17.gmap] * Output file : [GLIMPSE_impute/s18_imputed_LG17_10487008_16487194.bcf] * Output format : [BCF format | ZLIB compression] GLIMPSE_phase parameters: * Imputation model : [Reference panel imputation] * Input region : [LG17:10487008-16487194] * Output region : [LG17:11486965-15487122] * Sparse MAF : [0.001] * Recombination rates : [Given by genetic map] * Ploidy : [Only diploid samples in region] * Keep monom. ref sites: [NO] Model parameters: * #Burnin iterations : [5] * #Main iterations : [15] * Ne [eff. pop. size] : [100000] * Phase error rate : [0.0001] * Imputation error rate: [1e-12] * Min value for hap GLs: [1e-10] Selection parameters: * K init : [1000] * K pbwt : [2000] * PBWT depth : [12] * PBWT modulo (cM) : [0.1] * State list : [No list provided] Genotype calling: * Calling model : [standard] * Perform calling] BAM/CRAM filters and options: * Min mapping quality : [10] * Min base quality : [10] * Max depth : [40] * Keep failed QC : [NO] * Keep orphan reads : [NO] * Keep duplicate reads : [NO] * Keep supp. alignment : [NO] * Check pairing : [NO] * Ignore orientation : [NO] * Illumina-1.3+ : [NO] Other parameters * Seed : [15052011] * #Threads : [1] Initialisation: Parsing specified genomic regions * Input region [LG17:10487008-16487194] * Output region [LG17:11486965-15487122] * VCF/BCF scanning ... * VCF/BCF scanning [L=60483 (Lrare= 0 (0.0%) - Lcommon= 60483 (100.0%))] * VCF/BCF scanning [Nm=1 (Nmh=0 - Nmd=1) / Nr=126 (Nrh=0 - Nrd=126)] * VCF/BCF scanning [Reg=LG17:10487008-16487194 / L=60483] [0.00s] * Reference panel parsing ... ERROR: AC/AN INFO fields in VCF are inconsistent with GT field, update the values in the VCF [GLIMPSE2] Phase and impute low coverage sequencing data * Authors : Simone RUBINACCI & Olivier DELANEAU, University of Lausanne * Contact : simone.rubinacci@unil.ch & olivier.delaneau@unil.ch * Version : GLIMPSE2_phase v2.0.0 / commit = 3bed6d9 / release = 2022-12-07 * Citation : BiorXiv, (2022). DOI: https://doi.org/10.1101/2022.11.28.518213 * : Nature Genetics 53, 120–126 (2021). DOI: https://doi.org/10.1038/s41588-020-00756-0 * Run date : 24/01/2024 - 17:09:41 Files: * Input BAM/CRAM : [offspring/5X/5X_s18_sorted_chr17.bam] * Reference VCF : [BCFtools_Oni17_HD_Parents_pos_newinfo.bcf] * Genetic Map : [chr17.gmap] * Output file : [GLIMPSE_impute/s18_imputed_LG17_14488091_20488329.bcf] * Output format : [BCF format | ZLIB compression] GLIMPSE_phase parameters: * Imputation model : [Reference panel imputation] * Input region : [LG17:14488091-20488329] * Output region : [LG17:15488063-19488319] * Sparse MAF : [0.001] * Recombination rates : [Given by genetic map] * Ploidy : [Only diploid samples in region] * Keep monom. ref sites: [NO] Model parameters: * #Burnin iterations : [5] * #Main iterations : [15] * Ne [eff. pop. size] : [100000] * Phase error rate : [0.0001] * Imputation error rate: [1e-12] * Min value for hap GLs: [1e-10] Selection parameters: * K init : [1000] * K pbwt : [2000] * PBWT depth : [12] * PBWT modulo (cM) : [0.1] * State list : [No list provided] Genotype calling: * Calling model : [standard] * Perform calling] BAM/CRAM filters and options: * Min mapping quality : [10] * Min base quality : [10] * Max depth : [40] * Keep failed QC : [NO] * Keep orphan reads : [NO] * Keep duplicate reads : [NO] * Keep supp. alignment : [NO] * Check pairing : [NO] * Ignore orientation : [NO] * Illumina-1.3+ : [NO] Other parameters * Seed : [15052011] * #Threads : [1] Initialisation: Parsing specified genomic regions * Input region [LG17:14488091-20488329] * Output region [LG17:15488063-19488319] * VCF/BCF scanning ... * VCF/BCF scanning [L=60215 (Lrare= 0 (0.0%) - Lcommon= 60215 (100.0%))] * VCF/BCF scanning [Nm=1 (Nmh=0 - Nmd=1) / Nr=126 (Nrh=0 - Nrd=126)] * VCF/BCF scanning [Reg=LG17:14488091-20488329 / L=60215] [0.00s] * Reference panel parsing ... ERROR: AC/AN INFO fields in VCF are inconsistent with GT field, update the values in the VCF [GLIMPSE2] Phase and impute low coverage sequencing data * Authors : Simone RUBINACCI & Olivier DELANEAU, University of Lausanne * Contact : simone.rubinacci@unil.ch & olivier.delaneau@unil.ch * Version : GLIMPSE2_phase v2.0.0 / commit = 3bed6d9 / release = 2022-12-07 * Citation : BiorXiv, (2022). DOI: https://doi.org/10.1101/2022.11.28.518213 * : Nature Genetics 53, 120–126 (2021). DOI: https://doi.org/10.1038/s41588-020-00756-0 * Run date : 24/01/2024 - 17:09:41 Files: * Input BAM/CRAM : [offspring/5X/5X_s18_sorted_chr17.bam] * Reference VCF : [BCFtools_Oni17_HD_Parents_pos_newinfo.bcf] * Genetic Map : [chr17.gmap] * Output file : [GLIMPSE_impute/s18_imputed_LG17_18488288_25552246.bcf] * Output format : [BCF format | ZLIB compression] GLIMPSE_phase parameters: * Imputation model : [Reference panel imputation] * Input region : [LG17:18488288-25552246] * Output region : [LG17:19488512-24552061] * Sparse MAF : [0.001] * Recombination rates : [Given by genetic map] * Ploidy : [Only diploid samples in region] * Keep monom. ref sites: [NO] Model parameters: * #Burnin iterations : [5] * #Main iterations : [15] * Ne [eff. pop. size] : [100000] * Phase error rate : [0.0001] * Imputation error rate: [1e-12] * Min value for hap GLs: [1e-10] Selection parameters: * K init : [1000] * K pbwt : [2000] * PBWT depth : [12] * PBWT modulo (cM) : [0.1] * State list : [No list provided] Genotype calling: * Calling model : [standard] * Perform calling] BAM/CRAM filters and options: * Min mapping quality : [10] * Min base quality : [10] * Max depth : [40] * Keep failed QC : [NO] * Keep orphan reads : [NO] * Keep duplicate reads : [NO] * Keep supp. alignment : [NO] * Check pairing : [NO] * Ignore orientation : [NO] * Illumina-1.3+ : [NO] Other parameters * Seed : [15052011] * #Threads : [1] Initialisation: Parsing specified genomic regions * Input region [LG17:18488288-25552246] * Output region [LG17:19488512-24552061] * VCF/BCF scanning ... * VCF/BCF scanning [L=52249 (Lrare= 0 (0.0%) - Lcommon= 52249 (100.0%))] * VCF/BCF scanning [Nm=1 (Nmh=0 - Nmd=1) / Nr=126 (Nrh=0 - Nrd=126)] * VCF/BCF scanning [Reg=LG17:18488288-25552246 / L=52249] [0.00s] * Reference panel parsing ... ERROR: AC/AN INFO fields in VCF are inconsistent with GT field, update the values in the VCF [GLIMPSE2] Phase and impute low coverage sequencing data * Authors : Simone RUBINACCI & Olivier DELANEAU, University of Lausanne * Contact : simone.rubinacci@unil.ch & olivier.delaneau@unil.ch * Version : GLIMPSE2_phase v2.0.0 / commit = 3bed6d9 / release = 2022-12-07 * Citation : BiorXiv, (2022). DOI: https://doi.org/10.1101/2022.11.28.518213 * : Nature Genetics 53, 120–126 (2021). DOI: https://doi.org/10.1038/s41588-020-00756-0 * Run date : 24/01/2024 - 17:09:42 Files: * Input BAM/CRAM : [offspring/5X/5X_s18_sorted_chr17.bam] * Reference VCF : [BCFtools_Oni17_HD_Parents_pos_newinfo.bcf] * Genetic Map : [chr17.gmap] * Output file : [GLIMPSE_impute/s18_imputed_LG17_23552135_29552455.bcf] * Output format : [BCF format | ZLIB compression] GLIMPSE_phase parameters: * Imputation model : [Reference panel imputation] * Input region : [LG17:23552135-29552455] * Output region : [LG17:24552069-28552189] * Sparse MAF : [0.001] * Recombination rates : [Given by genetic map] * Ploidy : [Only diploid samples in region] * Keep monom. ref sites: [NO] Model parameters: * #Burnin iterations : [5] * #Main iterations : [15] * Ne [eff. pop. size] : [100000] * Phase error rate : [0.0001] * Imputation error rate: [1e-12] * Min value for hap GLs: [1e-10] Selection parameters: * K init : [1000] * K pbwt : [2000] * PBWT depth : [12] * PBWT modulo (cM) : [0.1] * State list : [No list provided] Genotype calling: * Calling model : [standard] * Perform calling] BAM/CRAM filters and options: * Min mapping quality : [10] * Min base quality : [10] * Max depth : [40] * Keep failed QC : [NO] * Keep orphan reads : [NO] * Keep duplicate reads : [NO] * Keep supp. alignment : [NO] * Check pairing : [NO] * Ignore orientation : [NO] * Illumina-1.3+ : [NO] Other parameters * Seed : [15052011] * #Threads : [1] Initialisation: Parsing specified genomic regions * Input region [LG17:23552135-29552455] * Output region [LG17:24552069-28552189] * VCF/BCF scanning ... * VCF/BCF scanning [L=55271 (Lrare= 0 (0.0%) - Lcommon= 55271 (100.0%))] * VCF/BCF scanning [Nm=1 (Nmh=0 - Nmd=1) / Nr=126 (Nrh=0 - Nrd=126)] * VCF/BCF scanning [Reg=LG17:23552135-29552455 / L=55271] [0.00s] * Reference panel parsing ... ERROR: AC/AN INFO fields in VCF are inconsistent with GT field, update the values in the VCF [GLIMPSE2] Phase and impute low coverage sequencing data * Authors : Simone RUBINACCI & Olivier DELANEAU, University of Lausanne * Contact : simone.rubinacci@unil.ch & olivier.delaneau@unil.ch * Version : GLIMPSE2_phase v2.0.0 / commit = 3bed6d9 / release = 2022-12-07 * Citation : BiorXiv, (2022). DOI: https://doi.org/10.1101/2022.11.28.518213 * : Nature Genetics 53, 120–126 (2021). DOI: https://doi.org/10.1038/s41588-020-00756-0 * Run date : 24/01/2024 - 17:09:42 Files: * Input BAM/CRAM : [offspring/5X/5X_s18_sorted_chr17.bam] * Reference VCF : [BCFtools_Oni17_HD_Parents_pos_newinfo.bcf] * Genetic Map : [chr17.gmap] * Output file : [GLIMPSE_impute/s18_imputed_LG17_27552155_35047771.bcf] * Output format : [BCF format | ZLIB compression] GLIMPSE_phase parameters: * Imputation model : [Reference panel imputation] * Input region : [LG17:27552155-35047771] * Output region : [LG17:28552197-34047604] * Sparse MAF : [0.001] * Recombination rates : [Given by genetic map] * Ploidy : [Only diploid samples in region] * Keep monom. ref sites: [NO] Model parameters: * #Burnin iterations : [5] * #Main iterations : [15] * Ne [eff. pop. size] : [100000] * Phase error rate : [0.0001] * Imputation error rate: [1e-12] * Min value for hap GLs: [1e-10] Selection parameters: * K init : [1000] * K pbwt : [2000] * PBWT depth : [12] * PBWT modulo (cM) : [0.1] * State list : [No list provided] Genotype calling: * Calling model : [standard] * Perform calling] BAM/CRAM filters and options: * Min mapping quality : [10] * Min base quality : [10] * Max depth : [40] * Keep failed QC : [NO] * Keep orphan reads : [NO] * Keep duplicate reads : [NO] * Keep supp. alignment : [NO] * Check pairing : [NO] * Ignore orientation : [NO] * Illumina-1.3+ : [NO] Other parameters * Seed : [15052011] * #Threads : [1] Initialisation: Parsing specified genomic regions * Input region [LG17:27552155-35047771] * Output region [LG17:28552197-34047604] * VCF/BCF scanning ... * VCF/BCF scanning [L=52109 (Lrare= 0 (0.0%) - Lcommon= 52109 (100.0%))] * VCF/BCF scanning [Nm=1 (Nmh=0 - Nmd=1) / Nr=126 (Nrh=0 - Nrd=126)] * VCF/BCF scanning [Reg=LG17:27552155-35047771 / L=52109] [0.00s] * Reference panel parsing ... ERROR: AC/AN INFO fields in VCF are inconsistent with GT field, update the values in the VCF [GLIMPSE2] Phase and impute low coverage sequencing data * Authors : Simone RUBINACCI & Olivier DELANEAU, University of Lausanne * Contact : simone.rubinacci@unil.ch & olivier.delaneau@unil.ch * Version : GLIMPSE2_phase v2.0.0 / commit = 3bed6d9 / release = 2022-12-07 * Citation : BiorXiv, (2022). DOI: https://doi.org/10.1101/2022.11.28.518213 * : Nature Genetics 53, 120–126 (2021). DOI: https://doi.org/10.1038/s41588-020-00756-0 * Run date : 24/01/2024 - 17:09:42 Files: * Input BAM/CRAM : [offspring/5X/5X_s18_sorted_chr17.bam] * Reference VCF : [BCFtools_Oni17_HD_Parents_pos_newinfo.bcf] * Genetic Map : [chr17.gmap] * Output file : [GLIMPSE_impute/s18_imputed_LG17_33047399_39041650.bcf] * Output format : [BCF format | ZLIB compression] GLIMPSE_phase parameters: * Imputation model : [Reference panel imputation] * Input region : [LG17:33047399-39041650] * Output region : [LG17:34047618-39041650] * Sparse MAF : [0.001] * Recombination rates : [Given by genetic map] * Ploidy : [Only diploid samples in region] * Keep monom. ref sites: [NO] Model parameters: * #Burnin iterations : [5] * #Main iterations : [15] * Ne [eff. pop. size] : [100000] * Phase error rate : [0.0001] * Imputation error rate: [1e-12] * Min value for hap GLs: [1e-10] Selection parameters: * K init : [1000] * K pbwt : [2000] * PBWT depth : [12] * PBWT modulo (cM) : [0.1] * State list : [No list provided] Genotype calling: * Calling model : [standard] * Perform calling] BAM/CRAM filters and options: * Min mapping quality : [10] * Min base quality : [10] * Max depth : [40] * Keep failed QC : [NO] * Keep orphan reads : [NO] * Keep duplicate reads : [NO] * Keep supp. alignment : [NO] * Check pairing : [NO] * Ignore orientation : [NO] * Illumina-1.3+ : [NO] Other parameters * Seed : [15052011] * #Threads : [1] Initialisation: Parsing specified genomic regions * Input region [LG17:33047399-39041650] * Output region [LG17:34047618-39041650] * VCF/BCF scanning ... * VCF/BCF scanning [L=45173 (Lrare= 0 (0.0%) - Lcommon= 45173 (100.0%))] * VCF/BCF scanning [Nm=1 (Nmh=0 - Nmd=1) / Nr=126 (Nrh=0 - Nrd=126)] * VCF/BCF scanning [Reg=LG17:33047399-39041650 / L=45173] [0.00s] * Reference panel parsing ... ERROR: AC/AN INFO fields in VCF are inconsistent with GT field, update the values in the VCF