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added usage description to README. added more keywords to setup. adde…
…d back the de novo files and co-segregate variant file inputs.
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| For detailed help/support, email Adam: | ||
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| [email protected] | ||
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| ## Usage Details | ||
| ### Input data | ||
| -m Standard .maf | ||
| -f Standard .vcf | ||
| -T Custom .tsv | ||
| Variant data may be input via at least one variant file. | ||
| This means that if variants are spread across several files, then you can input one of each type. | ||
| For the .maf and .tsv, use the custom columns to determine which columns to use. | ||
| Note that a standard .maf does not include protein annotations. | ||
| Use the custom column for the peptide change column. | ||
| If your .vcf has VEP annotations, then CharGer should be able to parse the information. | ||
| This information will be added to your variants when available. | ||
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| ### Output | ||
| -o output file | ||
| -w output as HTML (flag) | ||
| -k annotate input (flag) | ||
| --run-url-test test url when creating links | ||
| Name your output file; otherwise it will be called charger_summary.tsv. | ||
| You can opt to make the output into an HTML page, instead of a readable .tsv. | ||
| If you need to be assured of properly linked URL's, use the url test flag. | ||
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| ### Access data | ||
| -l ClinVar (flag) | ||
| -x ExAC (flag) | ||
| -E VEP (flag) | ||
| -t TCGA cancer types (flag) | ||
| Using these flags turns on accession features built in. | ||
| For the ClinVar, ExAC, and VEP flags, if no local VEP or databse is provided, then BioMine will be used to access the ReST interface. | ||
| The TCGA flag allows disease determination from sample barcodes in a .maf when using a diseases file (see below). | ||
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| ### Suppress data or overrides | ||
| -O override with ClinVar description (flag) | ||
| -D suppress needing disease specific (flag) | ||
| You can have CharGer override its pathogenic characterization with whatever ClinVar has. | ||
| Suppressing disease specific variants takes any variants in the diseases file (see below) and treats them as equally pathogenic without disease consideration. | ||
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| ### Cross-reference data | ||
| -z pathogenic variants, .vcf | ||
| -e expression matrix file, .tsv | ||
| -g gene list file, (format: gene\\tdisease\\tmode_of_inheritance) .txt | ||
| -d diseases file, (format: gene\\tdisease\\tmode_of_inheritance) .tsv | ||
| -n de novo file, standard .maf | ||
| -a assumed de novo file, standard .maf | ||
| -c co-segregation file, standard .maf | ||
| -H HotSpot3D clusters file, .clusters | ||
| -r recurrence threshold (default = 2) | ||
| Variants or genes from each of these files can be used as additional known information. | ||
| An expression matrix file has columns for each sample, and its rows are genes. | ||
| The genes should be approved HUGO symbols. | ||
| HotSpot3D clusters can be used for versions v1.x.x. | ||
| The recurrence threshold will be pulled from the recurrence/weight column of the .clusters file when provided. | ||
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| ### Local VEP | ||
| --vep-script Path to VEP | ||
| --vep-dir Path to VEP directory | ||
| --vep-cache Path to VEP cache directory | ||
| --vep-version VEP version (default = 87) | ||
| --vep-output VEP output file (default = charger.vep.vcf) | ||
| --grch assembly GRCh verion (default = 37) | ||
| --ensembl-release Ensembl release version (default = 75) | ||
| --reference-fasta VEP reference fasta | ||
| --fork Number of forked processes used in VEP (default = 0) | ||
| This currently only works with .vcf input only. | ||
| Annotations are run with the VEP everything flag, so any local plugins will be used. | ||
| The BioMine accession is also suppressed when using a local VEP installaltion. | ||
| The VEP directory is not the same as would be given to VEP's --dir option. | ||
| Instead it is the path to the directory with the VEP .pl file. | ||
| The VEP script is the .pl file only. | ||
| If not given, it will be /vep-dir/variant\_effect\_predictor.pl. | ||
| The VEP cache directory is the same as would be given to VEP's --dir-cache option. | ||
| If you have multiple VEP versions, then specify the version you want to use. | ||
| This can be different from the Ensembl release option. | ||
| VEP output is the same os would be given to VEP's -o option and should end with .vcf. | ||
| The default output file will be called charger.vep.vcf. | ||
| The GRCh reference genome can be set to either 37 or 38. | ||
| The reference Fasta file will be deteremined automatically if not specified. | ||
| If the reference Fasta file is constructed automatically, then if, for example, the VEP chache is ~/.vep/, the Ensembl release is 74, and the reference assembly is 37, then the reference Fasta file will be ~/.vep/homo\_sapiens/74\_GRCH37/Homo\_sapiens.GRCh37.74.dna.primary\_assembly.fa.gz. | ||
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| ### Local databases | ||
| --exac-vcf ExAC vcf.gz | ||
| --mac-clinvar-tsv ClinVar from MacArthur lab (clinvar_alleles.tsv.gz) | ||
| Using local databases suppresses the BioMine accession too. | ||
| These files can be downloaded from their respective sites. | ||
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| ### Filters | ||
| --rare Allele frequency threshold for rare/common (default = 1, process variant with any frequency): | ||
| --vcf-any-filter Allow variants that do not pass all filters in .vcf input (flag) | ||
| --mutation-types Comma delimited list of types to allow | ||
| Using filters will limit the variants processed. | ||
| The rare option takes variants with allele frequency less than the given value. | ||
| The .vcf any filter accepts only variants that have passed all filters. | ||
| If no .vcf pass filter status given, the .vcf null value will be taken as having passed. | ||
| Mutation types filtering requires a comma delimitted list (no spaces) using terms from Ensembl's consequence terms. | ||
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| ### ReST batch sizes | ||
| -v VEP (#variants, default/max allowed = 150) | ||
| -b ClinVar summary (#variants, default/max allowed = 500) | ||
| -B ClinVar searchsize (#variants, default/max allowed = 50) | ||
| ReST API's usually have limits on the amount of data sent or received. | ||
| Exceeding these batch sizes would normally lead to warnings and/or IP blockage, but CharGer and BioMine try to keep batches at safe sizes. Last updated limits February 2017. | ||
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| ### Custom columns (0-based) | ||
| -G HUGO gene symbol | ||
| -X chromosome | ||
| -S start position | ||
| -P stop position | ||
| -R reference allele | ||
| -A alternate allele | ||
| -s strand | ||
| -M sample name | ||
| -C codon | ||
| -p peptide change | ||
| -L variant classification | ||
| -F allele frequency | ||
| Use these for .tsv and/or .maf input variant files to specify columns of relevant data. | ||
| CharGer makes use of genomic and protein variant annotations, so the more data made available the better your results. | ||
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| #!/bin/python | ||
| # CharGer - Characterization of Germline variants | ||
| # author: Adam D Scott ([email protected]) & Kuan-lin Huang ([email protected]) | ||
| # version: v0.1.0 - 2015*12 | ||
| # version: v0.1.0 - 2016*04 | ||
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| import sys | ||
| import getopt | ||
| from charger import charger | ||
| import time | ||
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| def parseArgs( argv ): | ||
| helpText = "Usage: " | ||
| helpText = "\nCharGer - v0.1.0\n\n" | ||
| helpText += "Usage: " | ||
| helpText += "charger <input file> [options]\n\n" | ||
| helpText += "Accepted input data files:\n" | ||
| helpText += " -m Standard .maf\n" | ||
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| helpText += " -O override with ClinVar description (flag)\n" | ||
| helpText += " -D suppress needing disease specific (flag)\n" | ||
| helpText += "Cross-reference data files:\n" | ||
| helpText += " -z pathogenic variants .vcf\n" | ||
| helpText += " -e expression matrix file .tsv\n" | ||
| helpText += " -g gene list file .txt\n" | ||
| helpText += " -d diseases file (format: gene\\tdisease\\tmode_of_inheritance) .tsv\n" | ||
| helpText += " -n de novo file .?\n" | ||
| helpText += " -a assumed de novo file .?\n" | ||
| helpText += " -c co-segregation file .?\n" | ||
| helpText += " -H HotSpot3D clusters file .clusters\n" | ||
| helpText += " -r recurrence threshold (default = )\n" | ||
| helpText += " -z pathogenic variants, .vcf\n" | ||
| helpText += " -e expression matrix file, .tsv\n" | ||
| helpText += " -g gene list file, (format: gene\\tdisease\\tmode_of_inheritance) .txt\n" | ||
| helpText += " -d diseases file, (format: gene\\tdisease\\tmode_of_inheritance) .tsv\n" | ||
| helpText += " -n de novo file, standard .maf\n" | ||
| helpText += " -a assumed de novo file, standard .maf\n" | ||
| helpText += " -c co-segregation file, standard .maf\n" | ||
| helpText += " -H HotSpot3D clusters file, .clusters\n" | ||
| helpText += " -r recurrence threshold (default = 2)\n" | ||
| helpText += "Local VEP (works with .vcf input only; suppresses ReST too):\n" | ||
| helpText += " --vep-script Path to VEP\n" | ||
| helpText += " --vep-dir Path to VEP directory\n" | ||
| helpText += " --vep-cache Path to VEP cache directory\n" | ||
| helpText += " --vep-version VEP version (default = 87)\n" | ||
| helpText += " --vep-output VEP output file (default = charger.vep.vcf)\n" | ||
| helpText += " --grch assembly GRCh verion (default = 37)\n" | ||
| helpText += " --ensembl-release Ensembl release version (default = 74)\n" | ||
| helpText += " --ensembl-release Ensembl release version (default = 75)\n" | ||
| helpText += " --reference-fasta VEP reference fasta\n" | ||
| helpText += " --fork Number of forked processes used in VEP (default = 0) \n" | ||
| helpText += "Local databases (suppresses ReST too):\n" | ||
| helpText += " --exac-vcf ExAC vcf.gz\n" | ||
| #helpText += " --clinvar-tsv ClinVar (.tsv.gz download)\n" | ||
| #helpText += " --clinvar-vcf ClinVar (.vcf.gz download)\n" | ||
| helpText += " --mac-clinvar-tsv ClinVar from MacArthur lab (clinvar_alleles.tsv.gz)\n" | ||
| helpText += " --mac-clinvar-vcf ClinVar from MacArthur lab (clinvar_alleles.vcf.gz)\n" | ||
| #helpText += " --mac-clinvar-vcf ClinVar from MacArthur lab (clinvar_alleles.vcf.gz)\n" | ||
| helpText += "Filters:\n" | ||
| helpText += " --rare Allele frequency threshold for rare/common (default = 1, process variant with any frequency):\n" | ||
| helpText += " --vcf-any-filter Allow variants that do not pass all filters in .vcf input (flag)\n" | ||
| helpText += " --mutation-types Comma delimited list of types to allow\n" | ||
| helpText += " --mutation-types Comma delimited list (no spaces) of types to allow\n" | ||
| helpText += "ReST batch sizes:\n" | ||
| helpText += " -v VEP (#variants, default/max allowed = )\n" | ||
| helpText += " -v VEP (#variants, default/max allowed = 150)\n" | ||
| helpText += " -b ClinVar summary (#variants, default/max allowed = 500)\n" | ||
| helpText += " -B ClinVar searchsize (#variants, default/max allowed = 50)\n" | ||
| helpText += "Custom columns (0-based)\n" | ||
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