Skip to main content Link Search Menu Expand Document (external link)

phase

Table of contents

  1. Description
  2. Usage
  3. Command line options
    1. Basic options
    2. Input parameters
    3. Model parameters
    4. Selection parameters
    5. BAM/CRAM options and filters
    6. Output parameters

Description

Tool for imputation and phasing.

Usage

Simple run

GLIMPSE2_phase --bam-list bams_1.0x.txt --reference binary_reference_panel_chr20_7702567_12266861.bin --output imputed_glimpse2_rp140k_1.0x_chr20_7702567_12266861.bcf --threads 4

Command line options

Basic options

Option name Argument Default Description
--help NA NA Produces help message
--seed INT 15052011 Seed of the random number generator
-T [ --threads ] INT 1 Number of threads

Input parameters

Option name Argument Default Description
--bam-file FILE NA Input BAM/CRAM file containing low-coverage sequencing reads. Only one of the following options can be declared: --input-gl, --bam-file, --bam-list.
--bam-list FILE NA List (.txt file) of input BAM/CRAM files containing BAM/CRAM file containing low-coverage sequencing reads. One file per line. A second column (space separated) can be used to specify the sample name, otherwise the name of the file is used. Only one of the following options can be declared: --input-gl, --bam-file, --bam-list.
--input-gl FILE NA VCF/BCF file containing the genotype likelihoods. Only one of the following options can be declared: --input-gl, --bam-file, --bam-list.
-R [--reference] FILE NA Haplotype reference in VCF/BCF or binary format
-M [ --map ] FILE NA Genetic map
--input-region STRING NA Imputation region with buffers
--output-region STRING NA Imputation region without buffers
--sparse-maf FLOAT 0.001 Expert setting. Rare variant threshold
--samples-file STRING NA File with sample names and ploidy information. One sample per line with a mandatory second column indicating ploidy (1 or 2). Sample names that are not present are assumed to have ploidy 2 (diploids). If the parameter is omitted, all samples are assumed to be diploid. GLIMPSE does NOT handle the use of sex (M/F) instead of ploidy.
--ind-name STRING NA Only used together with --bam-file. Name of the sample to be processed. If not specified the prefix of the BAM/CRAM file (--bam-file) is used.
--keep-monomorphic-ref-sites NA NA Expert setting. Keeps monomorphic markers in the reference panel (removed by default)
--impute-reference-only-variants NA NA Only used together with --input-gl. Allows imputation at variants only present in the reference panel (no GL called at these positions). The use of this option is intended only to allow imputation at sporadic missing variants. If the number of missing variants is non-sporadic, please re-run the genotype likelihood computation at all reference variants and avoid using this option, since data from the reads should be used. A warning is thrown if reference-only variants are found.
--input-field-gl NA NA Only used together with --input-gl. Use FORMAT/GL field instead of FORMAT/PL to read genotyope likelihoods

Model parameters

Option name Argument Default Description
--burn-in INT 5 Expert setting. Number of burn-in iterations of the Gibbs sampler
--main INT 15 Expert setting. Number of main iterations of the Gibbs sampler
--ne INT 100000 Expert setting. Effective diploid population size modelling recombination frequency
--min-gl FLOAT 1e-10 Expert setting. Minimim haploid likelihood
--err-imp FLOAT 1e-12 Expert setting. Imputation HMM error rate
--err-phase FLOAT 1e-4 Expert setting. Phasing HMM error rate

Selection parameters

Option name Argument Default Description
--pbwt-depth INT 12 Expert setting. Number of neighbors in the sparse PBWT selection step (positive number).
--pbwt-modulo-cm FLOAT 5 Expert setting. Frequency of PBWT selection in cM (positive number). This parameter is automatically adjusted in case of small imputation regions.
--Kinit INT 1000 Expert setting. Number of states used for initialization (positive number). Can be set to zero only when –state-list is set, to skip the selection for the initialization step.
--Kpbwt INT 2000 Expert setting. Maximum number of states selected from the sparse PBWT (positive number). Can be set to zero only when –state-list is set, to skip the selection for during the Gibbs iterations.
--state-list FILE 5 Expert setting. List (.txt file) of haplotypes always present in the conditioning set, independent from state selection. Not affected by other selection parameters. Each row is a target haplotype (two lines per sample in case of diploid individuals) each column is a space separated list of reference haplotypes (in numerical order 0-(2N-1) ). Useful when prior knowledge of relatedness between the reference and target panel is known a priori.

BAM/CRAM options and filters

Option name Argument Default Description
--call-model STRING standard Model to use to call the data. Only the standard model is available at the moment.
--call-indels NA NA Expert setting. Use the calling model to produce genotype likelihoods at indels. However the likelihoods from low-coverage data can be miscalibrated, therefore by default GLIMPSE does only imputation into the haplotype scaffold (assuming flat likelihoods)
-F [ --fasta ] FILE NA Faidx-indexed reference sequence file in the appropriate genome build. Necessary for CRAM files
--mapq INT 10 Minimum mapping quality for a read to be considered
--baseq INT 10 Minimum phred-scalde based quality to be considered
--max-depth INT 40 Expert setting. Max read depth at a site. If the number of reads exceeds this number, the reads at the sites are downsampled (e.g. to avoid artifactual coverage increases).
--keep-orphan-reads NA NA Expert setting. Keep paired end reads where one of mates is unmapped
--ignore-orientation NA NA Expert setting. Ignore the orientation of mate pairs
--check-proper-pairing NA NA Expert setting. Discard reads that are not properly paired
--keep-failed-qc NA NA Expert setting. Keep reads that fail sequencing QC (as indicated by the sequencer).
--keep-duplicates NA NA Expert setting. Keep duplicate sequencing reads in the process
--illumina13+ NA NA Expert setting. Use illimina 1.3 encoding for the base quality (for older sequencing machines)

Output parameters

Option name Argument Default Description
-O [--output ] FILE NA Phased and imputed haplotypes in VCF/BCF/BGEN format
--contigs-fai FILE NA If specified, header contig names and their lengths are copied from the provided fasta index file (.fai). This allows to create imputed whole-genome files as contigs are present and can be easily merged by bcftools
--bgen-bits INT 8 Expert setting. Only used together when the output is in BGEN file format. Specifies the number of bits to be used for the encoding probabilities of the output BGEN file. If the output is in the .vcf[.gz]/.bcf format, this value is ignored. Accepted values: 1-32.
--bgen-compr STRING zstd Expert setting. Only used together when the output is in BGEN file format. Specifies the compression of the output BGEN file. If the output is in the .vcf[.gz]/.bcf format, this value is ignored. Accepted values: [no,zlib,zstd]
--log FILE NA Log file