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= Optional flags =
= Optional flags =
{| width="200" border="1" cellpadding="1" cellspacing="1"
Besides conforming to SAM specification, Karma developed its own optional tags to help evaluate mapping.
{| cellspacing="1" cellpadding="1" border="1" width="600"
|-
|-
| XA
| XA
| Alignment PathTag
| Alignment PathTag
|-
|-
| RG
| RG
| Sample GroupID
| Sample GroupID
|-
|-
| HA
| HA
| numMatchContributors (possible hits checked by karma)
| numMatchContributors (possible hits checked by karma)
|-
|-
| UQ
| UQ
| phred quality of this read, assuming it is mapped correctly
| phred quality of this read, assuming it is mapped correctly
|-
|-
| NB
| NB
| Number of equally best hits
| Number of equally best hits
|-
|-
| ER
| ER
| Different kind of errors when mapping
| Different kind of errors when mapping
|}
|}
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= Other test and check capabilities =
= Other test and check capabilities =
Upon successfully building references, you will obtain a list of reference files like below:
Upon successfully building references, you will obtain a list of reference files like below:
{| style="width: 571px; height: 288px" border="1" cellspacing="1" cellpadding="1" width="571"
{| cellspacing="1" cellpadding="1" border="1" width="571" style="width: 571px; height: 288px;"
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|-
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