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comparison leftalign.xml @ 35:a5937157062f draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 84c34980b4fd8454c1cc630be5d6a3c22a4a1ef3"
author iuc
date Sat, 07 May 2022 19:49:37 +0000
parents a7c9782130e8
children
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34:a7c9782130e8 35:a5937157062f
59 <test> 59 <test>
60 <param name="reference_source_selector" value="history" /> 60 <param name="reference_source_selector" value="history" />
61 <param name="ref_file" ftype="fasta" value="leftalign.fa"/> 61 <param name="ref_file" ftype="fasta" value="leftalign.fa"/>
62 <param name="input_bam" ftype="bam" value="left-align-input.bam"/> 62 <param name="input_bam" ftype="bam" value="left-align-input.bam"/>
63 <param name="iterations" value="5"/> 63 <param name="iterations" value="5"/>
64 <output name="output_bam" file="left-align-output.bam" /> 64 <output name="output_bam" file="left-align-output.bam" ftype="bam" lines_diff="2" />
65 </test> 65 </test>
66 </tests> 66 </tests>
67 <help> 67 <help>
68 68
69 When calling indels, it is important to homogenize the positional distribution of insertions and deletions in the input by using left realignment. Left realignment will place all indels in homopolymer and microsatellite repeats at the same position, provided that doing so does not introduce mismatches between the read and reference other than the indel. This method is computationally inexpensive and handles the most common classes of alignment inconsistency. 69 When calling indels, it is important to homogenize the positional distribution of insertions and deletions in the input by using left realignment. Left realignment will place all indels in homopolymer and microsatellite repeats at the same position, provided that doing so does not introduce mismatches between the read and reference other than the indel. This method is computationally inexpensive and handles the most common classes of alignment inconsistency.