Mercurial > repos > devteam > samtools_mpileup
diff samtools_mpileup.xml @ 2:3aa48bcbc599 draft
Uploaded tarball for 0.0.3 version.
| author | devteam |
|---|---|
| date | Wed, 12 Mar 2014 12:53:30 -0400 |
| parents | b47a418ccfdc |
| children | da0203c3461a |
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--- a/samtools_mpileup.xml Wed Mar 12 12:52:52 2014 -0400 +++ b/samtools_mpileup.xml Wed Mar 12 12:53:30 2014 -0400 @@ -1,30 +1,46 @@ -<tool id="samtools_mpileup" name="MPileup" version="0.0.2"> - <description>SNP and indel caller</description> - <requirements> - <requirement type="package" version="0.1.18">samtools</requirement> - </requirements> - <command interpreter="python">samtools_wrapper.py - -p 'samtools mpileup' - --stdout "${output_log}" +<tool id="samtools_mpileup" name="MPileup" version="0.0.3"> + <description>SNP and indel caller</description> + <requirements> + <requirement type="package" version="0.1.19">samtools</requirement> + </requirements> + <command><![CDATA[ + #if $reference_source.reference_source_selector == "history": + ln -s "${reference_source.ref_file}" && samtools faidx `basename "${reference_source.ref_file}"` && samtools mpileup + #else: + samtools mpileup + #end if #if $reference_source.reference_source_selector != "history": - -p '-f "${reference_source.ref_file.fields.path}"' + -f "${reference_source.ref_file.fields.path}" #else: - -d "-f" "${reference_source.ref_file}" "fa" "reference_input" + -f "${reference_source.ref_file}" #end if #for $i, $input_bam in enumerate( $reference_source.input_bams ): - -d " " "${input_bam.input_bam}" "${input_bam.input_bam.ext}" "bam_input_${i}" - -d "" "${input_bam.input_bam.metadata.bam_index}" "bam_index" "bam_input_${i}" ##hardcode galaxy ext type as bam_index + $input_bam.input_bam #end for - -p ' #if str( $advanced_options.advanced_options_selector ) == "advanced": - ${advanced_options.skip_anomalous_read_pairs} + #if str( $advanced_options.filter_by_flags.filter_flags ) == "filter": + #if $advanced_options.filter_by_flags.require_flags: + --rf ${sum([int(flag) for flag in str($advanced_options.filter_by_flags.require_flags).split(',')])} + #end if + #if $advanced_options.filter_by_flags.exclude_flags: + --ff ${sum([int(flag) for flag in str($advanced_options.filter_by_flags.exclude_flags).split(',')])} + #end if + #end if + #if str( $advanced_options.limit_by_region.limit_by_regions ) == "paste": + -l "$pasted_regions" + #elif str( $advanced_options.limit_by_region.limit_by_regions ) == "history" + -l "$bed_regions" + #end if + #if str( $advanced_options.exclude_read_group.exclude_read_groups ) == "paste": + -G "$excluded_read_groups" + #elif str( $advanced_options.exclude_read_group.exclude_read_groups ) == "history" + -G "$read_groups" + #end if + ${advanced_options.skip_anomalous_read_pairs} ${advanced_options.disable_probabilistic_realignment} -C "${advanced_options.coefficient_for_downgrading}" -d "${advanced_options.max_reads_per_bam}" ${advanced_options.extended_BAQ_computation} - #if str( $advanced_options.position_list ) != 'None': - -l "${advanced_options.position_list}" - #end if -q "${advanced_options.minimum_mapping_quality}" -Q "${advanced_options.minimum_base_quality}" #if str( $advanced_options.region_string ): @@ -40,6 +56,9 @@ -h "${genotype_likelihood_computation_type.coefficient_for_modeling_homopolymer_errors}" #if str( $genotype_likelihood_computation_type.perform_indel_calling.perform_indel_calling_selector ) == 'perform_indel_calling': -L "${genotype_likelihood_computation_type.perform_indel_calling.skip_indel_calling_above_sample_depth}" + -m "${genotype_likelihood_computation_type.perform_indel_calling.minimum_gapped_reads_for_indel_candidates}" + -F "${genotype_likelihood_computation_type.perform_indel_calling.minimum_gapped_read_fraction}" + ${genotype_likelihood_computation_type.perform_indel_calling.gapped_read_per_sample} #else: -I #end if @@ -47,159 +66,428 @@ #if len( $genotype_likelihood_computation_type.platform_list_repeat ): -P "${ ",".join( [ str( platform.platform_entry ) for platform in $genotype_likelihood_computation_type.platform_list_repeat ] ) }" #end if + #else: + ${genotype_likelihood_computation_type.base_position_on_reads} + ${genotype_likelihood_computation_type.output_mapping_quality} #end if - > "${output_mpileup}" - ' - </command> - <inputs> - <conditional name="reference_source"> - <param name="reference_source_selector" type="select" label="Choose the source for the reference list"> - <option value="cached">Locally cached</option> - <option value="history">History</option> - </param> - <when value="cached"> - <repeat name="input_bams" title="BAM file" min="1"> - <param name="input_bam" type="data" format="bam" label="BAM file"> - <validator type="unspecified_build" /> - <validator type="dataset_metadata_in_data_table" table_name="fasta_indexes" metadata_name="dbkey" metadata_column="1" message="Sequences are not currently available for the specified build." /> <!-- fixme!!! this needs to be a select --> - </param> - </repeat> - <param name="ref_file" type="select" label="Using reference genome"> - <options from_data_table="fasta_indexes"> - <!-- <filter type="data_meta" ref="input_bam" key="dbkey" column="1" /> does not yet work in a repeat...--> - </options> - </param> - </when> - <when value="history"> <!-- FIX ME!!!! --> - <repeat name="input_bams" title="BAM file" min="1"> - <param name="input_bam" type="data" format="bam" label="BAM file"> - <validator type="metadata" check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue." /> - </param> - </repeat> - <param name="ref_file" type="data" format="fasta" label="Using reference file" /> - </when> - </conditional> - - - <conditional name="genotype_likelihood_computation_type"> - <param name="genotype_likelihood_computation_type_selector" type="select" label="Genotype Likelihood Computation"> - <option value="perform_genotype_likelihood_computation">Perform genotype likelihood computation</option> - <option value="do_not_perform_genotype_likelihood_computation" selected="True">Do not perform genotype likelihood computation</option> - </param> - <when value="perform_genotype_likelihood_computation"> - <param name="gap_extension_sequencing_error_probability" type="integer" value="20" label="Phred-scaled gap extension sequencing error probability" /> - <param name="coefficient_for_modeling_homopolymer_errors" type="integer" value="100" label="Coefficient for modeling homopolymer errors." /> - <conditional name="perform_indel_calling"> - <param name="perform_indel_calling_selector" type="select" label="Perform INDEL calling"> - <option value="perform_indel_calling" selected="True">Perform INDEL calling</option> - <option value="do_not_perform_indel_calling">Do not perform INDEL calling</option> + > "$output_mpileup" 2> "$output_log" + ]]></command> + <stdio> + <exit_code range="1:" level="fatal" description="Error" /> + </stdio> + <inputs> + <conditional name="reference_source"> + <param name="reference_source_selector" type="select" label="Choose the source for the reference list"> + <option value="cached">Locally cached</option> + <option value="history">History</option> </param> - <when value="perform_indel_calling"> - <param name="skip_indel_calling_above_sample_depth" type="integer" value="250" label="Skip INDEL calling if the average per-sample depth is above" /> + <when value="cached"> + <repeat name="input_bams" title="BAM file" min="1"> + <param name="input_bam" type="data" format="bam" label="BAM file"> + <validator type="unspecified_build" /> + <validator type="dataset_metadata_in_data_table" table_name="fasta_indexes" metadata_name="dbkey" metadata_column="1" message="Sequences are not currently available for the specified build." /> <!-- fixme!!! this needs to be a select --> + </param> + </repeat> + <param name="ref_file" type="select" label="Using reference genome"> + <options from_data_table="fasta_indexes" /> + <!-- <filter type="data_meta" ref="input_bam" key="dbkey" column="1" /> does not yet work in a repeat...--> + </param> + </when> + <when value="history"> + <repeat name="input_bams" title="BAM file" min="1"> + <param name="input_bam" type="data" format="bam" label="BAM file"> + <validator type="metadata" check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue." /> + </param> + </repeat> + <param name="ref_file" type="data" format="fasta" label="Using reference file" /> + </when> + </conditional> + <conditional name="genotype_likelihood_computation_type"> + <param name="genotype_likelihood_computation_type_selector" type="select" label="Genotype Likelihood Computation"> + <option value="perform_genotype_likelihood_computation">Perform genotype likelihood computation</option> + <option value="do_not_perform_genotype_likelihood_computation" selected="True">Do not perform genotype likelihood computation</option> + </param> + <when value="perform_genotype_likelihood_computation"> + <param name="gap_extension_sequencing_error_probability" type="integer" value="20" label="Phred-scaled gap extension sequencing error probability" /> + <param name="coefficient_for_modeling_homopolymer_errors" type="integer" value="100" label="Coefficient for modeling homopolymer errors." /> + <conditional name="perform_indel_calling"> + <param name="perform_indel_calling_selector" type="select" label="Perform INDEL calling"> + <option value="perform_indel_calling" selected="True">Perform INDEL calling</option> + <option value="do_not_perform_indel_calling">Do not perform INDEL calling</option> + </param> + <when value="perform_indel_calling"> + <param name="skip_indel_calling_above_sample_depth" type="integer" value="250" label="Skip INDEL calling if the average per-sample depth is above" /> + <param name="minimum_gapped_reads_for_indel_candidates" type="integer" value="1" label="Minimum gapped reads for indel candidates" /> + <param name="minimum_gapped_read_fraction" type="float" value="0.002" label="Minimum fraction of gapped reads for candidates" /> + <param name="gapped_read_per_sample" type="boolean" truevalue="-p" falsevalue="" checked="False" label="Apply minimum values on a per-sample basis" /> + </when> + <when value="do_not_perform_indel_calling" /> + </conditional> + <param name="gap_open_sequencing_error_probability" type="integer" value="40" label="Phred-scaled gap open sequencing error probability" /> + <repeat name="platform_list_repeat" title="Platform for INDEL candidates"> + <param name="platform_entry" type="text" value="" label="Platform to use for INDEL candidates" /> + </repeat> + </when> + <when value="do_not_perform_genotype_likelihood_computation"> + <param name="base_position_on_reads" type="boolean" truevalue="-O" falsevalue="" checked="False" label="Output base positions on reads" /> + <param name="output_mapping_quality" type="boolean" truevalue="-s" falsevalue="" checked="False" label="Output mapping quality" /> </when> - <when value="do_not_perform_indel_calling" /> - </conditional> - <param name="gap_open_sequencing_error_probability" type="integer" value="40" label="Phred-scaled gap open sequencing error probability" /> - <repeat name="platform_list_repeat" title="Platform for INDEL candidates"> - <param name="platform_entry" type="text" value="" label="Platform to use for INDEL candidates" /> - </repeat> - </when> - <when value="do_not_perform_genotype_likelihood_computation"> - <!-- Do nothing here --> - </when> - </conditional> - <conditional name="advanced_options"> - <param name="advanced_options_selector" type="select" label="Set advanced options"> - <option value="basic" selected="True">Basic</option> - <option value="advanced">Advanced</option> - </param> - <when value="advanced"> - <param name="skip_anomalous_read_pairs" type="boolean" truevalue="-A" falsevalue="" checked="False" label="Do not skip anomalous read pairs in variant calling" /> - <param name="disable_probabilistic_realignment" type="boolean" truevalue="-B" falsevalue="" checked="False" label=" Disable probabilistic realignment for the computation of base alignment quality (BAQ)" /> - <param name="coefficient_for_downgrading" type="integer" value="0" label="Coefficient for downgrading mapping quality for reads containing excessive mismatches" /> - <param name="max_reads_per_bam" type="integer" value="250" label="Max reads per BAM" /> - <param name="extended_BAQ_computation" type="boolean" truevalue="-E" falsevalue="" checked="False" label="Extended BAQ computation" /> - <param name="position_list" type="data" format="bed" label="List of regions or sites on which to operate" optional="True" /> - <param name="minimum_mapping_quality" type="integer" value="0" label="Minimum mapping quality for an alignment to be used" /> - <param name="minimum_base_quality" type="integer" value="13" label="Minimum base quality for a base to be considered" /> - <param name="region_string" type="text" value="" label="Only generate pileup in region" /> - <param name="output_per_sample_read_depth" type="boolean" truevalue="-D" falsevalue="" checked="False" label="Output per-sample read depth" /> - <param name="output_per_sample_strand_bias_p_value" type="boolean" truevalue="-S" falsevalue="" checked="False" label="Output per-sample Phred-scaled strand bias P-value" /> - </when> - <when value="basic" /> - </conditional> - </inputs> - <outputs> - <data format="pileup" name="output_mpileup" label="${tool.name} on ${on_string}"> - <change_format> - <when input="genotype_likelihood_computation_type.genotype_likelihood_computation_type_selector" value="perform_genotype_likelihood_computation" format="bcf" /> - </change_format> - </data> - <data format="txt" name="output_log" label="${tool.name} on ${on_string} (log)" /> - </outputs> - <tests> - <test> - <param name="reference_source_selector" value="history" /> - <param name="ref_file" value="phiX.fasta" ftype="fasta" /> - <param name="input_bam" value="gatk/gatk_table_recalibration/gatk_table_recalibration_out_1.bam" ftype="bam" /> - <param name="genotype_likelihood_computation_type_selector" value="do_not_perform_genotype_likelihood_computation" /> - <param name="advanced_options_selector" value="basic" /> - <output name="output_mpileup" file="samtools/mpileup/samtools_mpileup_out_1.pileup" /> - <output name="output_log" file="samtools/mpileup/samtools_mpileup_out_1.log" /> - </test> - <test> - <param name="reference_source_selector" value="history" /> - <param name="ref_file" value="phiX.fasta" ftype="fasta" /> - <param name="input_bam" value="gatk/gatk_table_recalibration/gatk_table_recalibration_out_1.bam" ftype="bam" /> - <param name="genotype_likelihood_computation_type_selector" value="perform_genotype_likelihood_computation" /> - <param name="gap_extension_sequencing_error_probability" value="20" /> - <param name="coefficient_for_modeling_homopolymer_errors" value="100" /> - <param name="perform_indel_calling_selector" value="perform_indel_calling" /> - <param name="skip_indel_calling_above_sample_depth" value="250" /> - <param name="gap_open_sequencing_error_probability" value="40" /> - <param name="platform_list_repeat" value="0" /> - <param name="advanced_options_selector" value="basic" /> - <output name="output_mpileup" file="samtools/mpileup/samtools_mpileup_out_2.bcf" /> - <output name="output_log" file="samtools/mpileup/samtools_mpileup_out_1.log" /> - </test> - </tests> - <help> + </conditional> + <conditional name="advanced_options"> + <param name="advanced_options_selector" type="select" label="Set advanced options"> + <option value="basic" selected="True">Basic</option> + <option value="advanced">Advanced</option> + </param> + <when value="advanced"> + <conditional name="filter_by_flags"> + <param name="filter_flags" type="select" label="Set filter by flags"> + <option value="nofilter" selected="True">Do not filter</option> + <option value="filter">Filter by flags to exclude or require</option> + </param> + <when value="filter"> + <param name="require_flags" type="select" display="checkboxes" multiple="True" label="Require"> + <option value="1">Read is paired</option> + <option value="2">Read is mapped in a proper pair</option> + <option value="4">The read is unmapped</option> + <option value="8">The mate is unmapped</option> + <option value="16">Read strand</option> + <option value="32">Mate strand</option> + <option value="64">Read is the first in a pair</option> + <option value="128">Read is the second in a pair</option> + <option value="256">The alignment or this read is not primary</option> + <option value="512">The read fails platform/vendor quality checks</option> + <option value="1024">The read is a PCR or optical duplicate</option> + </param> + <param name="exclude_flags" type="select" display="checkboxes" multiple="True" label="Exclude"> + <option value="1">Read is paired</option> + <option value="2">Read is mapped in a proper pair</option> + <option value="4">The read is unmapped</option> + <option value="8">The mate is unmapped</option> + <option value="16">Read strand</option> + <option value="32">Mate strand</option> + <option value="64">Read is the first in a pair</option> + <option value="128">Read is the second in a pair</option> + <option value="256">The alignment or this read is not primary</option> + <option value="512">The read fails platform/vendor quality checks</option> + <option value="1024">The read is a PCR or optical duplicate</option> + </param> + </when> + <when value="nofilter" /> + </conditional> + <conditional name="limit_by_region"> + <param name="limit_by_regions" type="select" label="Select regions to call"> + <option value="no_limit" selected="True">Do not limit</option> + <option value="history">From an uploaded BED file</option> + <option value="paste">Paste a list of regions or BED</option> + </param> + <when value="history"> + <param name="bed_regions" type="data" format="bed" label="BED file"> + <validator type="dataset_ok_validator" /> + </param> + </when> + <when value="paste"> + <param name="region_paste" type="text" area="true" size="10x35" label="Regions" help="Paste a list of regions in BED format or as a list of chromosomes and positions"/> + </when> + <when value="no_limit" /> + </conditional> + <conditional name="exclude_read_group"> + <param name="exclude_read_groups" type="select" label="Select read groups to exclude"> + <option value="no_limit" selected="True">Do not exclude</option> + <option value="history">From an uploaded text file</option> + <option value="paste">Paste a list of read groups</option> + </param> + <when value="history"> + <param name="read_groups" type="data" format="txt" label="Text file"> + <validator type="dataset_ok_validator" /> + </param> + </when> + <when value="paste"> + <param name="group_paste" type="text" area="true" size="10x35" label="Read groups" help="Paste a list of read groups"/> + </when> + <when value="no_limit" /> + </conditional> + <param name="skip_anomalous_read_pairs" type="boolean" truevalue="-A" falsevalue="" checked="False" label="Do not skip anomalous read pairs in variant calling" /> + <param name="disable_probabilistic_realignment" type="boolean" truevalue="-B" falsevalue="" checked="False" label=" Disable probabilistic realignment for the computation of base alignment quality (BAQ)" /> + <param name="coefficient_for_downgrading" type="integer" value="0" label="Coefficient for downgrading mapping quality for reads containing excessive mismatches" /> + <param name="max_reads_per_bam" type="integer" value="250" label="Max reads per BAM" /> + <param name="extended_BAQ_computation" type="boolean" truevalue="-E" falsevalue="" checked="False" label="Extended BAQ computation" /> + <param name="minimum_mapping_quality" type="integer" value="0" label="Minimum mapping quality for an alignment to be used" /> + <param name="minimum_base_quality" type="integer" value="13" label="Minimum base quality for a base to be considered" /> + <param name="region_string" type="text" value="" label="Only generate pileup in region" /> + <param name="output_per_sample_read_depth" type="boolean" truevalue="-D" falsevalue="" checked="False" label="Output per-sample read depth" /> + <param name="output_per_sample_strand_bias_p_value" type="boolean" truevalue="-S" falsevalue="" checked="False" label="Output per-sample Phred-scaled strand bias P-value" /> + </when> + <when value="basic" /> + </conditional> + </inputs> + <configfiles> + <configfile name="excluded_read_groups"> +<![CDATA[ +<% +import re +%> +#set pasted_data = '' +#if str( $advanced_options.advanced_options_selector ) == "advanced": + #if str( $advanced_options.exclude_read_group.exclude_read_groups ) == "paste": + #set regex=re.compile("\\s+") + #set pasted_data = '\t'.join( regex.split( str( $advanced_options.exclude_read_group['read_groups'] ) ) ) + #end if +#end if +${pasted_data} +]]> + </configfile> + <configfile name="pasted_regions"> +<![CDATA[ +<% +import re +%> +#set pasted_data = '' +#if str( $advanced_options.advanced_options_selector ) == "advanced": + #if str( $advanced_options.limit_by_region.limit_by_regions ) == "paste": + #set regex=re.compile("\\s+") + #set pasted_data = '\t'.join( regex.split( str( $advanced_options.limit_by_region['region_paste'] ) ) ) + #end if +#end if +${pasted_data} +]]> + </configfile> + </configfiles> + <outputs> + <data format="pileup" name="output_mpileup" label="${tool.name} on ${on_string}"> + <change_format> + <when input="genotype_likelihood_computation_type.genotype_likelihood_computation_type_selector" value="perform_genotype_likelihood_computation" format="bcf" /> + </change_format> + </data> + <data format="txt" name="output_log" label="${tool.name} on ${on_string} (log)" /> + </outputs> + <tests> + <test> + <param name="reference_source_selector" value="history" /> + <param name="ref_file" value="phiX.fasta" ftype="fasta" /> + <param name="input_bam" value="samtools_mpileup_in_1.bam" ftype="bam" /> + <param name="genotype_likelihood_computation_type_selector" value="do_not_perform_genotype_likelihood_computation" /> + <param name="advanced_options_selector" value="basic" /> + <param name="base_position_on_reads" value="true" /> + <param name="output_mapping_quality" value="true" /> + <output name="output_mpileup" file="samtools_mpileup_out_1.pileup" /> + <output name="output_log" file="samtools_mpileup_out_1.log" /> + </test> + <test> + <param name="reference_source_selector" value="history" /> + <param name="ref_file" value="phiX.fasta" ftype="fasta" /> + <param name="input_bam" value="samtools_mpileup_in_1.bam" ftype="bam" /> + <param name="genotype_likelihood_computation_type_selector" value="perform_genotype_likelihood_computation" /> + <param name="gap_extension_sequencing_error_probability" value="20" /> + <param name="coefficient_for_modeling_homopolymer_errors" value="100" /> + <param name="perform_indel_calling_selector" value="perform_indel_calling" /> + <param name="skip_indel_calling_above_sample_depth" value="250" /> + <param name="gap_open_sequencing_error_probability" value="40" /> + <param name="platform_list_repeat" value="0" /> + <param name="advanced_options_selector" value="basic" /> + <output name="output_mpileup" ftype="bcf" file="samtools_mpileup_out_2.bcf" lines_diff="1" /> + <output name="output_log" file="samtools_mpileup_out_2.log" /> + </test> + <test> + <param name="reference_source_selector" value="cached" /> + <param name="input_bam" value="samtools_mpileup_in_3.bam" ftype="bam" dbkey="phiX" /> + <param name="genotype_likelihood_computation_type_selector" value="perform_genotype_likelihood_computation" /> + <param name="gap_extension_sequencing_error_probability" value="20" /> + <param name="coefficient_for_modeling_homopolymer_errors" value="100" /> + <param name="perform_indel_calling_selector" value="perform_indel_calling" /> + <param name="skip_indel_calling_above_sample_depth" value="250" /> + <param name="gap_open_sequencing_error_probability" value="40" /> + <param name="platform_list_repeat" value="0" /> + <param name="advanced_options_selector" value="basic" /> + <output name="output_mpileup" ftype="bcf" file="samtools_mpileup_out_2.bcf" lines_diff="1" /> + <output name="output_log" file="samtools_mpileup_out_3.log" /> + </test> + <test> + <param name="reference_source_selector" value="cached" /> + <param name="input_bam" value="samtools_mpileup_in_1.bam" ftype="bam" dbkey="phiX" /> + <param name="genotype_likelihood_computation_type_selector" value="perform_genotype_likelihood_computation" /> + <param name="gap_extension_sequencing_error_probability" value="20" /> + <param name="coefficient_for_modeling_homopolymer_errors" value="100" /> + <param name="perform_indel_calling_selector" value="perform_indel_calling" /> + <param name="skip_indel_calling_above_sample_depth" value="250" /> + <param name="gap_open_sequencing_error_probability" value="40" /> + <param name="platform_list_repeat" value="0" /> + <param name="advanced_options_selector" value="advanced" /> + <param name="advanced_options|filter_by_flags|filter_flags" value="nofilter" /> + <param name="advanced_options|limit_by_region|limit_by_regions" value="no_limit" /> + <param name="advanced_options|coefficient_for_downgrading" value="true" /> + <param name="advanced_options|max_reads_per_bam" value="200" /> + <param name="advanced_options|extended_BAQ_computation" value="true" /> + <param name="advanced_options|minimum_mapping_quality" value="0" /> + <param name="advanced_options|minimum_base_quality" value="43" /> + <output name="output_mpileup" ftype="bcf" file="samtools_mpileup_out_4.bcf" lines_diff="1" /> + <output name="output_log" file="samtools_mpileup_out_4.log" /> + </test> + </tests> + <help> **What it does** Generate BCF or pileup for one or multiple BAM files. Alignment records are grouped by sample identifiers in @RG header lines. If sample identifiers are absent, each input file is regarded as one sample. ------ -**Settings**:: +.. list-table:: **Input options** + :widths: 5 5 40 10 + :header-rows: 1 + + * - Flag + - Type + - Description + - Default + * - -6 + - *BOOLEAN* + - assume the quality is in the Illumina-1.3+ encoding + - off + * - -A + - *BOOLEAN* + - count anomalous read pairs + - off + * - -B + - *BOOLEAN* + - disable BAQ computation + - off + * - -b + - *FILE* + - list of input BAM filenames, one per line + - *null* + * - -C + - *INT* + - parameter for adjusting mapQ; 0 to disable + - 0 + * - -d + - *INT* + - max per-BAM depth to avoid excessive memory usage + - 250 + * - -E + - *BOOLEAN* + - recalculate extended BAQ on the fly thus ignoring existing BQs + - off + * - -f + - *FILE* + - faidx indexed reference sequence file + - *null* + * - -G + - *FILE* + - exclude read groups listed in FILE + - *null* + * - -l + - *FILE* + - list of positions (chr pos) or regions (BED) + - *null* + * - -M + - *INT* + - cap mapping quality at INT + - 60 + * - -r + - *STR* + - region in which pileup is generated + - *null* + * - -R + - *BOOLEAN* + - ignore RG tags + - off + * - -q + - *INT* + - skip alignments with mapQ smaller than INT + - 0 + * - -Q + - *INT* + - skip bases with baseQ/BAQ smaller than INT + - 13 + * - --rf + - *INT* + - required flags: skip reads with mask bits unset + - 0 + * - --ff + - *INT* + - filter flags: skip reads with mask bits set + - 0 + +------ - Input Options: - -6 Assume the quality is in the Illumina 1.3+ encoding. - -A Do not skip anomalous read pairs in variant calling. - -B Disable probabilistic realignment for the computation of base alignment quality (BAQ). BAQ is the Phred-scaled probability of a read base being misaligned. Applying this option greatly helps to reduce false SNPs caused by misalignments. - -b FILE List of input BAM files, one file per line [null] - -C INT Coefficient for downgrading mapping quality for reads containing excessive mismatches. Given a read with a phred-scaled probability q of being generated from the mapped position, the new mapping quality is about sqrt((INT-q)/INT)*INT. A zero value disables this functionality; if enabled, the recommended value for BWA is 50. [0] - -d INT At a position, read maximally INT reads per input BAM. [250] - -E Extended BAQ computation. This option helps sensitivity especially for MNPs, but may hurt specificity a little bit. - -f FILE The faidx-indexed reference file in the FASTA format. The file can be optionally compressed by razip. [null] - -l FILE BED or position list file containing a list of regions or sites where pileup or BCF should be generated [null] - -q INT Minimum mapping quality for an alignment to be used [0] - -Q INT Minimum base quality for a base to be considered [13] - -r STR Only generate pileup in region STR [all sites] - Output Options: - - -D Output per-sample read depth - -g Compute genotype likelihoods and output them in the binary call format (BCF). - -S Output per-sample Phred-scaled strand bias P-value - -u Similar to -g except that the output is uncompressed BCF, which is preferred for piping. - - Options for Genotype Likelihood Computation (for -g or -u): - - -e INT Phred-scaled gap extension sequencing error probability. Reducing INT leads to longer indels. [20] - -h INT Coefficient for modeling homopolymer errors. Given an l-long homopolymer run, the sequencing error of an indel of size s is modeled as INT*s/l. [100] - -I Do not perform INDEL calling - -L INT Skip INDEL calling if the average per-sample depth is above INT. [250] - -o INT Phred-scaled gap open sequencing error probability. Reducing INT leads to more indel calls. [40] - -P STR Comma dilimited list of platforms (determined by @RG-PL) from which indel candidates are obtained. It is recommended to collect indel candidates from sequencing technologies that have low indel error rate such as ILLUMINA. [all] +.. list-table:: **Output options** + :widths: 5 5 40 10 + :header-rows: 1 + + * - Flag + - Type + - Description + - Default + * - -D + - *BOOLEAN* + - output per-sample DP in BCF (require -g/-u) + - off + * - -g + - *BOOLEAN* + - generate BCF output (genotype likelihoods) + - off + * - -O + - *BOOLEAN* + - output base positions on reads (disabled by -g/-u) + - off + * - -s + - *BOOLEAN* + - output mapping quality (disabled by -g/-u) + - off + * - -S + - *BOOLEAN* + - output per-sample strand bias P-value in BCF (require -g/-u) + - off + * - -u + - *BOOLEAN* + - generate uncompressed BCF output + - off + +------ + +.. list-table:: **SNP/INDEL genotype likelihoods options (effective with '-g' or '-u')** + :widths: 5 5 40 10 + :header-rows: 1 + + * - Flag + - Type + - Description + - Default + * - -e + - *INT* + - Phred-scaled gap extension seq error probability + - 20 + * - -F + - *FLOAT* + - minimum fraction of gapped reads for candidates + - 0.002 + * - -h + - *INT* + - coefficient for homopolymer errors + - 100 + * - -I + - *BOOLEAN* + - do not perform indel calling + - off + * - -L + - *INT* + - max per-sample depth for INDEL calling + - 250 + * - -m + - *INT* + - minimum gapped reads for indel candidates + - 1 + * - -o + - *INT* + - Phred-scaled gap open sequencing error probability + - 40 + * - -p + - *BOOLEAN* + - apply -m and -F per-sample to increase sensitivity + - off + * - -P + - *STR* + - comma separated list of platforms for indels + - all ------ @@ -207,7 +495,7 @@ For the underlying tool, please cite `Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15;25(16):2078-9. <http://www.ncbi.nlm.nih.gov/pubmed/19505943>`_ + If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.* - - </help> -</tool> + </help> +</tool> \ No newline at end of file