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view DumpSTR/dumpSTR.xml @ 0:ecf8c4f9f8ba draft
"planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
author | michal_klinka |
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date | Sat, 23 Apr 2022 16:34:03 +0000 |
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children | 8e8cf43f6836 |
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<?xml version="1.0" ?> <tool id="dumpSTR" name="DumpSTR" version="@tool_version@"> <description>DumpSTR filters VCF files with TR genotypes, performing call-level and locus-level filtering, and outputs a filtered VCF file. </description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"/> <version_command>dumpSTR --version</version_command> <command detect_errors="exit_code"><![CDATA[dumpSTR ## h definition #if $options.h: -h #end if ## end h definition ## vcf definition #if $input_output.vcf: --vcf $input_output.vcf #end if ## end vcf definition ## out definition #if $input_output.out: --out $input_output.out #end if ## end out definition ## zip definition #if $input_output.zip: --zip #end if ## end zip definition ## vcftype definition #if $input_output.vcftype: --vcftype $input_output.vcftype #end if ## end vcftype definition ## min_locus_callrate definition #if $locus_level_filters__tool_agnostic_.min_locus_callrate: --min-locus-callrate $locus_level_filters__tool_agnostic_.min_locus_callrate #end if ## end min_locus_callrate definition ## min_locus_hwep definition #if $locus_level_filters__tool_agnostic_.min_locus_hwep: --min-locus-hwep $locus_level_filters__tool_agnostic_.min_locus_hwep #end if ## end min_locus_hwep definition ## min_locus_het definition #if $locus_level_filters__tool_agnostic_.min_locus_het: --min-locus-het $locus_level_filters__tool_agnostic_.min_locus_het #end if ## end min_locus_het definition ## max_locus_het definition #if $locus_level_filters__tool_agnostic_.max_locus_het: --max-locus-het $locus_level_filters__tool_agnostic_.max_locus_het #end if ## end max_locus_het definition ## use_length definition #if $locus_level_filters__tool_agnostic_.use_length: --use-length #end if ## end use_length definition ## filter_regions definition #if $locus_level_filters__tool_agnostic_.filter_regions: --filter-regions $locus_level_filters__tool_agnostic_.filter_regions #end if ## end filter_regions definition ## filter_regions_names definition #if $locus_level_filters__tool_agnostic_.filter_regions_names: --filter-regions-names $locus_level_filters__tool_agnostic_.filter_regions_names #end if ## end filter_regions_names definition ## filter_hrun definition #if $locus_level_filters__tool_agnostic_.filter_hrun: --filter-hrun #end if ## end filter_hrun definition ## drop_filtered definition #if $locus_level_filters__tool_agnostic_.drop_filtered: --drop-filtered #end if ## end drop_filtered definition ## hipstr_max_call_flank_indel definition #if $call_level_filters_specific_to_hipstr_output.hipstr_max_call_flank_indel: --hipstr-max-call-flank-indel $call_level_filters_specific_to_hipstr_output.hipstr_max_call_flank_indel #end if ## end hipstr_max_call_flank_indel definition ## hipstr_max_call_stutter definition #if $call_level_filters_specific_to_hipstr_output.hipstr_max_call_stutter: --hipstr-max-call-stutter $call_level_filters_specific_to_hipstr_output.hipstr_max_call_stutter #end if ## end hipstr_max_call_stutter definition ## hipstr_min_supp_reads definition #if $call_level_filters_specific_to_hipstr_output.hipstr_min_supp_reads: --hipstr-min-supp-reads $call_level_filters_specific_to_hipstr_output.hipstr_min_supp_reads #end if ## end hipstr_min_supp_reads definition ## hipstr_min_call_DP definition #if $call_level_filters_specific_to_hipstr_output.hipstr_min_call_DP: --hipstr-min-call-DP $call_level_filters_specific_to_hipstr_output.hipstr_min_call_DP #end if ## end hipstr_min_call_DP definition ## hipstr_max_call_DP definition #if $call_level_filters_specific_to_hipstr_output.hipstr_max_call_DP: --hipstr-max-call-DP $call_level_filters_specific_to_hipstr_output.hipstr_max_call_DP #end if ## end hipstr_max_call_DP definition ## hipstr_min_call_Q definition #if $call_level_filters_specific_to_hipstr_output.hipstr_min_call_Q: --hipstr-min-call-Q $call_level_filters_specific_to_hipstr_output.hipstr_min_call_Q #end if ## end hipstr_min_call_Q definition ## gangstr_min_call_DP definition #if $call_level_filters_specific_to_gangstr_output.gangstr_min_call_DP: --gangstr-min-call-DP $call_level_filters_specific_to_gangstr_output.gangstr_min_call_DP #end if ## end gangstr_min_call_DP definition ## gangstr_max_call_DP definition #if $call_level_filters_specific_to_gangstr_output.gangstr_max_call_DP: --gangstr-max-call-DP $call_level_filters_specific_to_gangstr_output.gangstr_max_call_DP #end if ## end gangstr_max_call_DP definition ## gangstr_min_call_Q definition #if $call_level_filters_specific_to_gangstr_output.gangstr_min_call_Q: --gangstr-min-call-Q $call_level_filters_specific_to_gangstr_output.gangstr_min_call_Q #end if ## end gangstr_min_call_Q definition ## gangstr_expansion_prob_het definition #if $call_level_filters_specific_to_gangstr_output.gangstr_expansion_prob_het: --gangstr-expansion-prob-het $call_level_filters_specific_to_gangstr_output.gangstr_expansion_prob_het #end if ## end gangstr_expansion_prob_het definition ## gangstr_expansion_prob_hom definition #if $call_level_filters_specific_to_gangstr_output.gangstr_expansion_prob_hom: --gangstr-expansion-prob-hom $call_level_filters_specific_to_gangstr_output.gangstr_expansion_prob_hom #end if ## end gangstr_expansion_prob_hom definition ## gangstr_expansion_prob_total definition #if $call_level_filters_specific_to_gangstr_output.gangstr_expansion_prob_total: --gangstr-expansion-prob-total $call_level_filters_specific_to_gangstr_output.gangstr_expansion_prob_total #end if ## end gangstr_expansion_prob_total definition ## gangstr_filter_span_only definition #if $call_level_filters_specific_to_gangstr_output.gangstr_filter_span_only: --gangstr-filter-span-only #end if ## end gangstr_filter_span_only definition ## gangstr_filter_spanbound_only definition #if $call_level_filters_specific_to_gangstr_output.gangstr_filter_spanbound_only: --gangstr-filter-spanbound-only #end if ## end gangstr_filter_spanbound_only definition ## gangstr_filter_badCI definition #if $call_level_filters_specific_to_gangstr_output.gangstr_filter_badCI: --gangstr-filter-badCI #end if ## end gangstr_filter_badCI definition ## gangstr_readlen definition #if $call_level_filters_specific_to_gangstr_output.gangstr_readlen: --gangstr-readlen $call_level_filters_specific_to_gangstr_output.gangstr_readlen #end if ## end gangstr_readlen definition ## advntr_min_call_DP definition #if $call_level_filters_specific_to_advntr_output.advntr_min_call_DP: --advntr-min-call-DP $call_level_filters_specific_to_advntr_output.advntr_min_call_DP #end if ## end advntr_min_call_DP definition ## advntr_max_call_DP definition #if $call_level_filters_specific_to_advntr_output.advntr_max_call_DP: --advntr-max-call-DP $call_level_filters_specific_to_advntr_output.advntr_max_call_DP #end if ## end advntr_max_call_DP definition ## advntr_min_spanning definition #if $call_level_filters_specific_to_advntr_output.advntr_min_spanning: --advntr-min-spanning $call_level_filters_specific_to_advntr_output.advntr_min_spanning #end if ## end advntr_min_spanning definition ## advntr_min_flanking definition #if $call_level_filters_specific_to_advntr_output.advntr_min_flanking: --advntr-min-flanking $call_level_filters_specific_to_advntr_output.advntr_min_flanking #end if ## end advntr_min_flanking definition ## advntr_min_ML definition #if $call_level_filters_specific_to_advntr_output.advntr_min_ML: --advntr-min-ML $call_level_filters_specific_to_advntr_output.advntr_min_ML #end if ## end advntr_min_ML definition ## eh_min_ADFL definition #if $call_level_filters_specific_to_expansionhunter_output.eh_min_ADFL: --eh-min-ADFL $call_level_filters_specific_to_expansionhunter_output.eh_min_ADFL #end if ## end eh_min_ADFL definition ## eh_min_ADIR definition #if $call_level_filters_specific_to_expansionhunter_output.eh_min_ADIR: --eh-min-ADIR $call_level_filters_specific_to_expansionhunter_output.eh_min_ADIR #end if ## end eh_min_ADIR definition ## eh_min_ADSP definition #if $call_level_filters_specific_to_expansionhunter_output.eh_min_ADSP: --eh-min-ADSP $call_level_filters_specific_to_expansionhunter_output.eh_min_ADSP #end if ## end eh_min_ADSP definition ## eh_min_call_LC definition #if $call_level_filters_specific_to_expansionhunter_output.eh_min_call_LC: --eh-min-call-LC $call_level_filters_specific_to_expansionhunter_output.eh_min_call_LC #end if ## end eh_min_call_LC definition ## eh_max_call_LC definition #if $call_level_filters_specific_to_expansionhunter_output.eh_max_call_LC: --eh-max-call-LC $call_level_filters_specific_to_expansionhunter_output.eh_max_call_LC #end if ## end eh_max_call_LC definition ## popstr_min_call_DP definition #if $call_level_filters_specific_to_popstr_output.popstr_min_call_DP: --popstr-min-call-DP $call_level_filters_specific_to_popstr_output.popstr_min_call_DP #end if ## end popstr_min_call_DP definition ## popstr_max_call_DP definition #if $call_level_filters_specific_to_popstr_output.popstr_max_call_DP: --popstr-max-call-DP $call_level_filters_specific_to_popstr_output.popstr_max_call_DP #end if ## end popstr_max_call_DP definition ## popstr_require_support definition #if $call_level_filters_specific_to_popstr_output.popstr_require_support: --popstr-require-support $call_level_filters_specific_to_popstr_output.popstr_require_support #end if ## end popstr_require_support definition ## num_records definition #if $debugging_parameters.num_records: --num-records $debugging_parameters.num_records #end if ## end num_records definition ## die_on_warning definition #if $debugging_parameters.die_on_warning: --die-on-warning #end if ## end die_on_warning definition ## verbose definition #if $debugging_parameters.verbose: --verbose #end if ## end verbose definition ## version definition #if $version313f.version: --version #end if ## end version definition 1>$stdout 2>$stderr ]]></command> <inputs> <section name="options" title="options" expanded="false"> <param argument="-h" type="boolean" optional="true" label="help" help="show this help message and exit"/> </section> <section name="input_output" title="Input/output" expanded="false"> <param argument="--vcf" type="data" format="vcf" optional="false" label="vcf" help="Input STR VCF file"/> <param argument="--out" type="text" optional="false" label="out" help="Prefix for output files"/> <param argument="--zip" type="boolean" optional="true" label="zip" help="Produce a bgzipped and tabix indexed output VCF"/> <param argument="--vcftype" type="select" optional="true" label="vcftype" help="Genotyper that was used to create this VCF input"> <expand macro="vcfTypes"/> </param> </section> <section name="locus_level_filters__tool_agnostic_" title="Locus-level filters (tool agnostic)" expanded="false"> <param argument="--min-locus-callrate" type="float" optional="true" label="min_locus_callrate" help="Minimum locus call rate"/> <param argument="--min-locus-hwep" type="float" optional="true" label="min_locus_hwep" help="Filter loci failing HWE at this p-value threshold"/> <param argument="--min-locus-het" type="float" optional="true" label="min_locus_het" help="Minimum locus heterozygosity"/> <param argument="--max-locus-het" type="float" optional="true" label="max_locus_het" help="Maximum locus heterozygosity"/> <param argument="--use-length" type="boolean" optional="true" label="use_length" help="Calculate per-locus stats (het, HWE) collapsing alleles by length"/> <param argument="--filter-regions" type="text" optional="true" label="filter_regions" help="Comma-separated list of BED files of regions to filter. Must be bgzipped and tabix indexed"/> <param argument="--filter-regions-names" type="text" optional="true" label="filter_regions_names" help="Comma-separated list of filter names for each BED filter file"/> <param argument="--filter-hrun" type="boolean" optional="true" label="filter_hrun" help="Filter STRs with long homopolymer runs."/> <param argument="--drop-filtered" type="boolean" optional="true" label="drop_filtered" help="Drop filtered records from output"/> </section> <section name="call_level_filters_specific_to_hipstr_output" title="Call-level filters specific to HipSTR output" expanded="false"> <param argument="--hipstr-max-call-flank-indel" type="float" optional="true" label="hipstr_max_call_flank_indel" help="Maximum call flank indel rate"/> <param argument="--hipstr-max-call-stutter" type="float" optional="true" label="hipstr_max_call_stutter" help="Maximum call stutter rate"/> <param argument="--hipstr-min-supp-reads" type="integer" optional="true" label="hipstr_min_supp_reads" help="Minimum supporting reads for each allele"/> <param argument="--hipstr-min-call-DP" type="integer" optional="true" label="hipstr_min_call_DP" help="Minimum call coverage"/> <param argument="--hipstr-max-call-DP" type="integer" optional="true" label="hipstr_max_call_DP" help="Maximum call coverage"/> <param argument="--hipstr-min-call-Q" type="float" optional="true" label="hipstr_min_call_Q" help="Minimum call quality score"/> </section> <section name="call_level_filters_specific_to_gangstr_output" title="Call-level filters specific to GangSTR output" expanded="false"> <param argument="--gangstr-min-call-DP" type="integer" optional="true" label="gangstr_min_call_DP" help="Minimum call coverage"/> <param argument="--gangstr-max-call-DP" type="integer" optional="true" label="gangstr_max_call_DP" help="Maximum call coverage"/> <param argument="--gangstr-min-call-Q" type="float" optional="true" label="gangstr_min_call_Q" help="Minimum call quality score"/> <param argument="--gangstr-expansion-prob-het" type="float" optional="true" label="gangstr_expansion_prob_het" help="Expansion prob-value threshold. Filters calls with probability of heterozygous expansion less than this"/> <param argument="--gangstr-expansion-prob-hom" type="float" optional="true" label="gangstr_expansion_prob_hom" help="Expansion prob-value threshold. Filters calls with probability of homozygous expansion less than this"/> <param argument="--gangstr-expansion-prob-total" type="float" optional="true" label="gangstr_expansion_prob_total" help="Expansion prob-value threshold. Filters calls with probability of total expansion less than this"/> <param argument="--gangstr-filter-span-only" type="boolean" optional="true" label="gangstr_filter_span_only" help="Filter out all calls that only have spanning read support"/> <param argument="--gangstr-filter-spanbound-only" type="boolean" optional="true" label="gangstr_filter_spanbound_only" help="Filter out all reads except spanning and bounding"/> <param argument="--gangstr-filter-badCI" type="boolean" optional="true" label="gangstr_filter_badCI" help="Filter regions where the ML estimate is not in the CI"/> <param argument="--gangstr-readlen" type="integer" optional="true" label="gangstr_readlen" help="Read length used (bp). Required if using --require-support"/> </section> <section name="call_level_filters_specific_to_advntr_output" title="Call-level filters specific to adVNTR output" expanded="false"> <param argument="--advntr-min-call-DP" type="integer" optional="true" label="advntr_min_call_DP" help="Minimum call coverage"/> <param argument="--advntr-max-call-DP" type="integer" optional="true" label="advntr_max_call_DP" help="Maximum call coverage"/> <param argument="--advntr-min-spanning" type="integer" optional="true" label="advntr_min_spanning" help="Minimum spanning read count (SR field)"/> <param argument="--advntr-min-flanking" type="integer" optional="true" label="advntr_min_flanking" help="Minimum flanking read count (FR field)"/> <param argument="--advntr-min-ML" type="float" optional="true" label="advntr_min_ML" help="Minimum value of maximum likelihood (ML field)"/> </section> <section name="call_level_filters_specific_to_expansionhunter_output" title="Call-level filters specific to ExpansionHunter output" expanded="false"> <param argument="--eh-min-ADFL" type="integer" optional="true" label="eh_min_ADFL" help="Minimum number of flanking reads consistent with the allele"/> <param argument="--eh-min-ADIR" type="integer" optional="true" label="eh_min_ADIR" help="Minimum number of in-repeat reads consistent with the allele"/> <param argument="--eh-min-ADSP" type="integer" optional="true" label="eh_min_ADSP" help="Minimum number of spanning reads consistent with the allele"/> <param argument="--eh-min-call-LC" type="integer" optional="true" label="eh_min_call_LC" help="Minimum call coverage"/> <param argument="--eh-max-call-LC" type="integer" optional="true" label="eh_max_call_LC" help="Maximum call coverage"/> </section> <section name="call_level_filters_specific_to_popstr_output" title="Call-level filters specific to PopSTR output" expanded="false"> <param argument="--popstr-min-call-DP" type="integer" optional="true" label="popstr_min_call_DP" help="Minimum call coverage"/> <param argument="--popstr-max-call-DP" type="integer" optional="true" label="popstr_max_call_DP" help="Maximum call coverage"/> <param argument="--popstr-require-support" type="integer" optional="true" label="popstr_require_support" help="Require each allele call to have at least n supporting reads"/> </section> <section name="debugging_parameters" title="Debugging parameters" expanded="false"> <param argument="--num-records" type="integer" optional="true" label="num_records" help="Only process this many records"/> <param argument="--die-on-warning" type="boolean" optional="true" label="die_on_warning" help="Quit if a record can't be parsed"/> <param argument="--verbose" type="boolean" optional="true" label="verbose" help="Print out extra info"/> </section> <section name="version313f" title="Version" expanded="false"> <param argument="--version" type="boolean" optional="true" label="version" help="show program's version number and exit"/> </section> </inputs> <outputs> <data name="stdout" label="STDOUT output" format="txt"/> <data name="main_output" label="Main output"> <discover_datasets format="vcf" pattern="(?P<designation>.+)\.vcf" visible="true" assign_primary_output="true"/> <discover_datasets format="tabular" pattern="(?P<designation>.+)\.tab" visible="true"/> </data> <data name="stderr" label="STDERR output" format="txt"> <discover_datasets format="vcf_bgzip" pattern="(?P<designation>.+)\.vcf.gz" visible="true"/> <discover_datasets format="tabix" pattern="(?P<designation>.+)\.vcf.gz.tbi" visible="true"/> </data> </outputs> <tests> <test> <section name="main_params"> <param name="vcf" value="NA12891_chr21_hipstr.sorted.vcf.gz"/> <param name="out" value="test_result"/> <param name="vcftype" value="hipstr"/> <param name="zip" value="false"/> </section> <section name="filter_opt"> <param name="min_locus_callrate" value="0.1"/> <param name="use_length" value="true"/> <param name="drop_filtered" value="true"/> </section> <section name="filter_call_level"> <section name="hipstr_filters"> <param name="hipstr_max_call_flank_indel" value="0.2"/> <param name="hipstr_min_call_Q" value="0.4"/> </section> </section> <output name="stdout" file="stdout.txt"/> <output name="main_output"> <discovered_dataset designation="test_result.loclog" file="test_result.loclog.tab"/> <discovered_dataset designation="test_result.samplog" file="test_result.samplog.tab"/> <discovered_dataset designation="test_result"> <assert_contents> <has_size value="4061730" delta="200"/> <has_text text="##fileformat=VCFv4.1"/> <has_n_lines n="9046"/> </assert_contents> </discovered_dataset> </output> <output name="stderr" file="stderr.txt"/> </test> </tests> <help>usage: main.py [-h] --vcf VCF --out OUT [--zip] [--vcftype VCFTYPE] [--min-locus-callrate MIN_LOCUS_CALLRATE] [--min-locus-hwep MIN_LOCUS_HWEP] [--min-locus-het MIN_LOCUS_HET] [--max-locus-het MAX_LOCUS_HET] [--use-length] [--filter-regions FILTER_REGIONS] [--filter-regions-names FILTER_REGIONS_NAMES] [--filter-hrun] [--drop-filtered] [--hipstr-max-call-flank-indel HIPSTR_MAX_CALL_FLANK_INDEL] [--hipstr-max-call-stutter HIPSTR_MAX_CALL_STUTTER] [--hipstr-min-supp-reads HIPSTR_MIN_SUPP_READS] [--hipstr-min-call-DP HIPSTR_MIN_CALL_DP] [--hipstr-max-call-DP HIPSTR_MAX_CALL_DP] [--hipstr-min-call-Q HIPSTR_MIN_CALL_Q] [--gangstr-min-call-DP GANGSTR_MIN_CALL_DP] [--gangstr-max-call-DP GANGSTR_MAX_CALL_DP] [--gangstr-min-call-Q GANGSTR_MIN_CALL_Q] [--gangstr-expansion-prob-het GANGSTR_EXPANSION_PROB_HET] [--gangstr-expansion-prob-hom GANGSTR_EXPANSION_PROB_HOM] [--gangstr-expansion-prob-total GANGSTR_EXPANSION_PROB_TOTAL] [--gangstr-filter-span-only] [--gangstr-filter-spanbound-only] [--gangstr-filter-badCI] [--gangstr-readlen GANGSTR_READLEN] [--advntr-min-call-DP ADVNTR_MIN_CALL_DP] [--advntr-max-call-DP ADVNTR_MAX_CALL_DP] [--advntr-min-spanning ADVNTR_MIN_SPANNING] [--advntr-min-flanking ADVNTR_MIN_FLANKING] [--advntr-min-ML ADVNTR_MIN_ML] [--eh-min-ADFL EH_MIN_ADFL] [--eh-min-ADIR EH_MIN_ADIR] [--eh-min-ADSP EH_MIN_ADSP] [--eh-min-call-LC EH_MIN_CALL_LC] [--eh-max-call-LC EH_MAX_CALL_LC] [--popstr-min-call-DP POPSTR_MIN_CALL_DP] [--popstr-max-call-DP POPSTR_MAX_CALL_DP] [--popstr-require-support POPSTR_REQUIRE_SUPPORT] [--num-records NUM_RECORDS] [--die-on-warning] [--verbose] [--version] options: -h, --help show this help message and exit Input/output: --vcf VCF Input STR VCF file --out OUT Prefix for output files --zip Produce a bgzipped and tabix indexed output VCF --vcftype VCFTYPE ##!!## Name trh could not be loaded Locus-level filters (tool agnostic): --min-locus-callrate MIN_LOCUS_CALLRATE Minimum locus call rate --min-locus-hwep MIN_LOCUS_HWEP Filter loci failing HWE at this p-value threshold --min-locus-het MIN_LOCUS_HET Minimum locus heterozygosity --max-locus-het MAX_LOCUS_HET Maximum locus heterozygosity --use-length Calculate per-locus stats (het, HWE) collapsing alleles by length --filter-regions FILTER_REGIONS Comma-separated list of BED files of regions to filter. Must be bgzipped and tabix indexed --filter-regions-names FILTER_REGIONS_NAMES Comma-separated list of filter names for each BED filter file --filter-hrun Filter STRs with long homopolymer runs. --drop-filtered Drop filtered records from output Call-level filters specific to HipSTR output: --hipstr-max-call-flank-indel HIPSTR_MAX_CALL_FLANK_INDEL Maximum call flank indel rate --hipstr-max-call-stutter HIPSTR_MAX_CALL_STUTTER Maximum call stutter rate --hipstr-min-supp-reads HIPSTR_MIN_SUPP_READS Minimum supporting reads for each allele --hipstr-min-call-DP HIPSTR_MIN_CALL_DP Minimum call coverage --hipstr-max-call-DP HIPSTR_MAX_CALL_DP Maximum call coverage --hipstr-min-call-Q HIPSTR_MIN_CALL_Q Minimum call quality score Call-level filters specific to GangSTR output: --gangstr-min-call-DP GANGSTR_MIN_CALL_DP Minimum call coverage --gangstr-max-call-DP GANGSTR_MAX_CALL_DP Maximum call coverage --gangstr-min-call-Q GANGSTR_MIN_CALL_Q Minimum call quality score --gangstr-expansion-prob-het GANGSTR_EXPANSION_PROB_HET Expansion prob-value threshold. Filters calls with probability of heterozygous expansion less than this --gangstr-expansion-prob-hom GANGSTR_EXPANSION_PROB_HOM Expansion prob-value threshold. Filters calls with probability of homozygous expansion less than this --gangstr-expansion-prob-total GANGSTR_EXPANSION_PROB_TOTAL Expansion prob-value threshold. Filters calls with probability of total expansion less than this --gangstr-filter-span-only Filter out all calls that only have spanning read support --gangstr-filter-spanbound-only Filter out all reads except spanning and bounding --gangstr-filter-badCI Filter regions where the ML estimate is not in the CI --gangstr-readlen GANGSTR_READLEN Read length used (bp). Required if using --require-support Call-level filters specific to adVNTR output: --advntr-min-call-DP ADVNTR_MIN_CALL_DP Minimum call coverage --advntr-max-call-DP ADVNTR_MAX_CALL_DP Maximum call coverage --advntr-min-spanning ADVNTR_MIN_SPANNING Minimum spanning read count (SR field) --advntr-min-flanking ADVNTR_MIN_FLANKING Minimum flanking read count (FR field) --advntr-min-ML ADVNTR_MIN_ML Minimum value of maximum likelihood (ML field) Call-level filters specific to ExpansionHunter output: --eh-min-ADFL EH_MIN_ADFL Minimum number of flanking reads consistent with the allele --eh-min-ADIR EH_MIN_ADIR Minimum number of in-repeat reads consistent with the allele --eh-min-ADSP EH_MIN_ADSP Minimum number of spanning reads consistent with the allele --eh-min-call-LC EH_MIN_CALL_LC Minimum call coverage --eh-max-call-LC EH_MAX_CALL_LC Maximum call coverage Call-level filters specific to PopSTR output: --popstr-min-call-DP POPSTR_MIN_CALL_DP Minimum call coverage --popstr-max-call-DP POPSTR_MAX_CALL_DP Maximum call coverage --popstr-require-support POPSTR_REQUIRE_SUPPORT Require each allele call to have at least n supporting reads Debugging parameters: --num-records NUM_RECORDS Only process this many records --die-on-warning Quit if a record can't be parsed --verbose Print out extra info Version: --version show program's version number and exit </help> <citations> <citation type="bibtex">@misc{TRTools: a toolkit for genome-wide analysis of tandem repeats, author = {Nima Mousavi, Jonathan Margoliash, Neha Pusarla, Shubham Saini, Richard Yanicky, Melissa Gymrek}, year = {2020}, title = {TRTools}, publisher = {GitHub}, journal = {GitHub repository}, url = {https://github.com/gymreklab/trtools}, } </citation> </citations> </tool>