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comparison samtools_mpileup.xml @ 15:32f6fffbc3e9 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_mpileup commit c508c3af0f4121dcc38e0be63db00a604e997b8a
author iuc
date Thu, 19 Jun 2025 13:00:51 +0000
parents b61f5d6a7f25
children 7df230bec125
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14:b61f5d6a7f25 15:32f6fffbc3e9
1 <tool id="samtools_mpileup" name="Samtools mpileup" version="2.1.7" profile="@PROFILE@"> 1 <tool id="samtools_mpileup" name="Samtools mpileup" version="2.1.8" profile="@PROFILE@">
2 <description>multi-way pileup of variants</description> 2 <description>multi-way pileup of variants</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
185 </conditional> 185 </conditional>
186 <conditional name="limit_by_region"> 186 <conditional name="limit_by_region">
187 <param name="limit_by_regions" value="limit"/> 187 <param name="limit_by_regions" value="limit"/>
188 <param name="region_paste" value="17:1050-1060" /> 188 <param name="region_paste" value="17:1050-1060" />
189 </conditional> 189 </conditional>
190 <param name="disable_probabilistic_realignment" value="-B" /> 190 <param name="disable_probabilistic_realignment" value="true" />
191 </conditional> 191 </conditional>
192 <output name="output_file_pu" file="mpileup.out.3" ftype="pileup" /> 192 <output name="output_file_pu" file="mpileup.out.3" ftype="pileup" />
193 </test> 193 </test>
194 <!-- test_cmd($opts,out=>'dat/mpileup.out.3',cmd=>"$$opts{bin}/samtools mpileup -B \-\-ff 0x14 -f $$opts{tmp}/mpileup.ref.fa.gz -r17:1050-1060 $$opts{tmp}/mpileup.1.bam | grep -v mpileup"); 194 <!-- test_cmd($opts,out=>'dat/mpileup.out.3',cmd=>"$$opts{bin}/samtools mpileup -B \-\-ff 0x14 -f $$opts{tmp}/mpileup.ref.fa.gz -r17:1050-1060 $$opts{tmp}/mpileup.1.bam | grep -v mpileup");
195 --> 195 -->
219 <conditional name="output_options_cond"> 219 <conditional name="output_options_cond">
220 <param name="output_options_selector" value="default" /> 220 <param name="output_options_selector" value="default" />
221 </conditional> 221 </conditional>
222 <conditional name="advanced_options"> 222 <conditional name="advanced_options">
223 <param name="advanced_options_selector" value="advanced" /> 223 <param name="advanced_options_selector" value="advanced" />
224 <param name="skip_anomalous_read_pairs" value="-A" /> 224 <param name="skip_anomalous_read_pairs" value="true" />
225 </conditional> 225 </conditional>
226 <output name="output_file_pu" file="samtools_mpileup_out_2.pileup" ftype="pileup" /> 226 <output name="output_file_pu" file="samtools_mpileup_out_2.pileup" ftype="pileup" />
227 </test> 227 </test>
228 <test> 228 <test>
229 <param name="input" ftype="bam" value="samtools_mpileup_in_1.bam" /> 229 <param name="input" ftype="bam" value="samtools_mpileup_in_1.bam" />
266 266
267 Note that there are two orthogonal ways to specify locations in the input file; via -r region and -l file. The former uses (and requires) an index to do random access while the latter streams through the file contents filtering out the specified regions, requiring no index. The two may be used in conjunction. For example a BED file containing locations of genes in chromosome 20 could be specified using -r 20 -l chr20.bed, meaning that the index is used to find chromosome 20 and then it is filtered for the regions listed in the bed file. 267 Note that there are two orthogonal ways to specify locations in the input file; via -r region and -l file. The former uses (and requires) an index to do random access while the latter streams through the file contents filtering out the specified regions, requiring no index. The two may be used in conjunction. For example a BED file containing locations of genes in chromosome 20 could be specified using -r 20 -l chr20.bed, meaning that the index is used to find chromosome 20 and then it is filtered for the regions listed in the bed file.
268 268
269 **BAQ (Base Alignment Quality)** 269 **BAQ (Base Alignment Quality)**
270 270
271 BAQ is the Phred-scaled probability of a read base being misaligned. It greatly helps to reduce false SNPs caused by misalignments. BAQ is calculated using the probabilistic realignment method described in the paper “Improving SNP discovery by base alignment quality”, Heng Li, Bioinformatics, Volume 27, Issue 8 <https://doi.org/10.1093/bioinformatics/btr076> 271 BAQ is the Phred-scaled probability of a read base being misaligned. It greatly helps to reduce false SNPs caused by misalignments. BAQ is calculated using the probabilistic realignment method described in the paper “Improving SNP discovery by base alignment quality”, Heng Li, Bioinformatics, Volume 27, Issue 8
272 272
273 BAQ is turned on when a reference file is supplied using the -f option. To disable it, use the -B option. 273 BAQ is turned on when a reference file is supplied using the -f option. To disable it, use the -B option.
274 274
275 It is possible to store pre-calculated BAQ values in a SAM BQ:Z tag. Samtools mpileup will use the precalculated values if it finds them. The -E option can be used to make it ignore the contents of the BQ:Z tag and force it to recalculate the BAQ scores by making a new alignment. 275 It is possible to store pre-calculated BAQ values in a SAM BQ:Z tag. Samtools mpileup will use the precalculated values if it finds them. The -E option can be used to make it ignore the contents of the BQ:Z tag and force it to recalculate the BAQ scores by making a new alignment.
276 ]]></help> 276 ]]></help>