96
edits
Changes
From Genome Analysis Wiki
Jump to navigationJump to search→Download Karma
<br> '''K-tuple Alignment with Rapid Matching Algorithm'''
<!-- BANNER ACROSS TOP OF PAGE -->
{| style="width:100%; background:#ffb6c1; margin-top:1.2em; border:1px solid #ccc;" |
| style="width:100%; text-align:center; white-space:nowrap; color:#000;" |
<div style="font-size:162%; border:none; margin:0; padding:.1em; color:#000;">KARMA is obsolete and not maintained</div>
|}
'''K-tuple Alignment with Rapid Matching Algorithm'''
Karma uses an existing reference to align short reads, such as those generated by Illumina sequencers.
Karma uses an existing reference to align short reads, such as those generated by Illumina sequencers.
= Download Karma =
= Download Karma =
To get a copy go to [http://www.sph.umich.edu/csg/pha/karma/download/ Karma Download]
To get a copy go to [http://csg.sph.umich.edu//pha/karma/download/ Karma Download]
= Build Karma =
= Build Karma =
= 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" style="width: 1034px; height: 291px;"
|-
|-
| 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:
ER:Z:no_match -> UNSET_QUALITY<br>ER:Z:invalid_bases -> INVALID_DATA (not used yet)<br>ER:Z:duplicates -> EARLYSTOP_DUPLICATES ( early stop due to reaching max number of best matches, with all bases matched)<br>ER:Z:quality -> EARLYSTOP_QUALITY (early stop due to reaching max posterior quality)<br>ER:Z:repeats -> REPEAT_QUALITY (not used yet)<br>
|}
|}
<br>
<br>
<br>
= Other test and check capabilities =
= Other test and check capabilities =
-s [int] -> set random number seed [12345]
-s [int] -> set random number seed [12345]
= Karma File structure =
= Karma file structure =
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;"
|-
|-
|
|
<br>
<br>
<br>
<br>
= Karma TODO List =
= Karma TODO List =
