Read Mapping parameters
You can adjust the following read mapping parameters to optimize your analysis results when you create or edit analysis workflows.
IMPORTANT! Use the default parameter settings unless you are an advanced user.
Variant Name |
Description |
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Flag to indicate whether mapped BAM files should be remapped. |
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Specifies the mismatch penalty. |
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Specifies the type of soft-clipping to perform. |
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Specifies the gap open penalty. |
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Specifies the match score. |
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Specifies the gap extension penalty. |
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Realign with context-dependent gap scores. |
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The maximum number of bases allowed for a read to overrun the end of the amplicon. |
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Specifies the flow score penalty. |
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Specifies to perform 3' soft-clipping (via -g) if at most this # of adapter bases were found. |
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Specifies the Local band width. |
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Trim repetitive sequence at the ends of alignment. |
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Specifies to perform 3' end repair. |
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Use bed file to capture INDELs near amplicon edges. |
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Specifies the output filter for the mapping. |
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The maximum INDEL size to rescue with one large INDEL algorithm. |