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comparison leftalign.xml @ 17:fcd4f3bf844e draft

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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 19:48:56 +0000
parents a2feedafda6f
children ed8508ec9613
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16:a2feedafda6f 17:fcd4f3bf844e
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.