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| MCHap | ||
| ===== | ||
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| Micro-haplotype assembly and manipulation | ||
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| Polyploid micro-haplotype assembly using Markov chain Monte Carlo simulation. | ||
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| Usage | ||
| ----- | ||
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| The wrapper CLI tool is ``mchap`` and assembly sub-tool is ``assemble``. | ||
| At minimum this tool requires the following inputs: | ||
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| - One or more bam files of reads aligned to a reference genome | ||
| - A bed file of target genomic loci for assembly | ||
| - An indexed VCF file containing a 'reference set' of SNPs | ||
| - An indexed fasta file containing the reference genome | ||
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| The ``assemble`` sub-tool writes out an uncompressed VCF file to standard output. | ||
| This should generally be compressed and written to a file: | ||
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| :: | ||
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| $ mchap assemble ... | bgzip > haplotypes.vcf.gz | ||
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| The full list of ``assemble`` arguments can be seen in the help text: | ||
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| :: | ||
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| $ mchap assemble -h | ||
| usage: MCMC haplotype assembly [-h] [--targets TARGETS] [--variants VARIANTS] | ||
| [--reference REFERENCE] [--bam [BAM [BAM ...]]] | ||
| [--bam-list BAM_LIST] [--ploidy PLOIDY] | ||
| [--sample-ploidy SAMPLE_PLOIDY] | ||
| [--sample-list SAMPLE_LIST] | ||
| [--error-rate ERROR_RATE] [--best-genotype] | ||
| [--call-filtered] [--mcmc-chains MCMC_CHAINS] | ||
| [--mcmc-steps MCMC_STEPS] | ||
| [--mcmc-burn MCMC_BURN] | ||
| [--mcmc-fix-homozygous MCMC_FIX_HOMOZYGOUS] | ||
| [--mcmc-seed MCMC_SEED] | ||
| [--filter-depth FILTER_DEPTH] | ||
| [--filter-read-count FILTER_READ_COUNT] | ||
| [--filter-probability FILTER_PROBABILITY] | ||
| [--filter-kmer-k FILTER_KMER_K] | ||
| [--filter-kmer FILTER_KMER] | ||
| [--read-group-field READ_GROUP_FIELD] | ||
| [--cores CORES] | ||
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| optional arguments: | ||
| -h, --help show this help message and exit | ||
| --targets TARGETS Bed file containing genomic intervals for haplotype | ||
| assembly. First three columns (contig, start, stop) | ||
| are mandatory. If present, the fourth column (id) will | ||
| be used as the variant id in the output VCF. | ||
| --variants VARIANTS Tabix indexed VCF file containing SNP variants to be | ||
| used in assembly. Assembled haplotypes will only | ||
| contain the reference and alternate alleles specified | ||
| within this file. | ||
| --reference REFERENCE | ||
| Indexed fasta file containing the reference genome. | ||
| --bam [BAM [BAM ...]] | ||
| A list of 0 or more bam files. Haplotypes will be | ||
| assembled for all samples found within all listed bam | ||
| files unless the --sample-list parameter is used. | ||
| --bam-list BAM_LIST A file containing a list of bam file paths (one per | ||
| line). This can optionally be used in place of or | ||
| combined with the --bam parameter. | ||
| --ploidy PLOIDY Default ploidy for all samples (default = 2). This | ||
| value is used for all samples which are not specified | ||
| using the --sample-ploidy parameter | ||
| --sample-ploidy SAMPLE_PLOIDY | ||
| A file containing a list of samples with a ploidy | ||
| value used to indicate where their ploidy differs from | ||
| the default value. Each line should contain a sample | ||
| identifier followed by a tab and then an integer | ||
| ploidy value. | ||
| --sample-list SAMPLE_LIST | ||
| Optionally specify a file containing a list of samples | ||
| to haplotype (one sample id per line). This file also | ||
| specifies the sample order in the output. If not | ||
| specified, all samples in the input bam files will be | ||
| haplotyped. | ||
| --error-rate ERROR_RATE | ||
| Expected base-call error rate of sequences in addition | ||
| to base phred scores (default = 0.0). By default only | ||
| the phred score of each base call is used to calculate | ||
| its probability of an incorrect call. The --error-rate | ||
| value is added to that probability. | ||
| --best-genotype Flag: allways call the best supported complete | ||
| genotype within a called phenotype. This may result in | ||
| calling genotypes with a posterior probability less | ||
| than --filter-probability however a phenotype | ||
| probability of >= --filter-probability is still | ||
| required. | ||
| --call-filtered Flag: include genotype calls for filtered samples. | ||
| Sample filter tags will still indicate samples that | ||
| have been filtered. WARNING: this can result in a | ||
| large VCF file with un-informative genotype calls. | ||
| --mcmc-chains MCMC_CHAINS | ||
| Number of independent MCMC chains per assembly | ||
| (default = 2). | ||
| --mcmc-steps MCMC_STEPS | ||
| Number of steps to simulate in each MCMC chain | ||
| (default = 1000). | ||
| --mcmc-burn MCMC_BURN | ||
| Number of initial steps to discard from each MCMC | ||
| chain (default = 500). | ||
| --mcmc-fix-homozygous MCMC_FIX_HOMOZYGOUS | ||
| Fix alleles that are homozygous with a probability | ||
| greater than or equal to the specified value (default | ||
| = 0.999). The probability of that a variant is | ||
| homozygous in a sample is assessed independently for | ||
| each variant prior to MCMC simulation. If an allele is | ||
| "fixed" it is not allowed vary within the MCMC thereby | ||
| reducing computational complexity. | ||
| --mcmc-seed MCMC_SEED | ||
| Random seed for MCMC (default = 42). | ||
| --filter-depth FILTER_DEPTH | ||
| Minimum sample read depth required to include an | ||
| assembly result (default = 5.0). Read depth is | ||
| measured as the mean of read depth across each | ||
| variable position. | ||
| --filter-read-count FILTER_READ_COUNT | ||
| Minimum number of read (pairs) required within a | ||
| target interval in order to include an assembly result | ||
| (default = 5). | ||
| --filter-probability FILTER_PROBABILITY | ||
| Minimum sample assembly posterior probability required | ||
| to call a phenotype i.e. a set of unique haplotypes of | ||
| unknown dosage (default = 0.95). Genotype dosage will | ||
| be called or partially called if it also exceeds this | ||
| threshold. See also the --best-genotype flag. | ||
| --filter-kmer-k FILTER_KMER_K | ||
| Size of variant kmer used to filter assembly results | ||
| (default = 3). | ||
| --filter-kmer FILTER_KMER | ||
| Minimum kmer representation required at each position | ||
| in assembly results (default = 0.90). | ||
| --read-group-field READ_GROUP_FIELD | ||
| Read group field to use as sample id (default = "SM"). | ||
| The chosen field determines tha sample ids required in | ||
| other input files e.g. the --sample-list argument. | ||
| --cores CORES Number of cpu cores to use (default = 2). |
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