HomeCLC FAQ - Import, export, and downloadsImport and Export of SAM/BAMHow can I import sequence reads in a SAM or BAM file?

2.1. How can I import sequence reads in a SAM or BAM file?

You can import the sequencing reads from a BAM file into the CLC Genomics and Biomedical Genomics Workbenches using the standard importer:

File | Import | Standard import

Please leave the import type set to Automatic.

After completing the import wizard, a popup window will appear asking you if you would like to skip importing this BAM file. Please click No in this popup window.

The imported data from the BAM file will be a single Sequence List, or can be multiple Sequence Lists - one for each Read Group in the BAM file. 

 

For paired data imported this way, we recommend that you go to the Element Info view of your data set to check, and where necessary, reset the minimum and maximum distance values. The values set by default are:

  • where a PI tag is present in the SAM/BAM file, the insert size range is set as:

maximum = 2 * PI tag value
minimum  = 1/2 * PI tag value

  • where there is no PI tag in the SAM/BAM file, the Workbench default distances are used: minimum 1, maximum 1000.

Setting the paired read distance range is described here:
http://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=General_notes_on_handling_paired_data.html

 

 

Knowledge Tags
sam  /  bam  /  Torrent  / 

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