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Support for Genome Workbench will end on March 31 2024. You may still use the application, but supporting documentation will not be available after this date. Read more.

BAM haplotype filtering

Step 1: Copy BAM file URL

Copy the sample BAM file URL address.

Click the Open command in the File menu.

Select BAM/CSRA files tab.

Paste the BAM file URL address into the Genome Workbench Open dialog (or just open the Genome Workbench sample file and skip the tutorial steps 1-3).

open bam

Click Next>.

Step 2: Map it to assembly GRCh37

Select the Use Mapping check box.

Click the Find Assembly button.

Type "GCF_000001405.13" in the Search term box and click the Find Assemblies button.

Select the row with the desired accession in the search results.

Select Assembly

Click OK button.

Map To GRCh37

Click Next>.

Step 3: Select Sequence NC_000001.10

Type "NC_000001.10" in the Filter box and press Enter.

Select Sequence

Click Next>. Click Finish to create a new project.

Step 4: Open Graphical Sequence View for NC_000001.10

Double-click the NC_000001.10 project item under Data folder in the Project View on the left.

Click the Graphical Sequence View line.

Ignore the warning message by clicking OK.

Step 5: Activate alignment track NA24385_hg19_phased_possorted_bam

Click the Configure Tracks icon.

Configure Tracks

Type "NA24385_hg19_phased_possorted_bam" in the Search box and press Enter.

Select the track with the same name and click OK.

Step 6: Zoom to a level where individual alignments are displayed (e.g. 19565K-19572K).

Right-click anywhere below the ruler. In the pop-up menu select the Go to Sequence Position/Range command. In the pop-up dialog type in "19565K-19572K" to the Sequence Position/Range box. Click the Go button. Click the Close button to close the dialog.

Step 7: Enable sorting by haplotype:

Click the Content Icon in the right upper corner of the alignment track. CContent Icon

Select the Sort alignments by haplotype command.

Sort By Haploype

The alignment tracks must show 3 subtracks:

Sorted Haplotypes

Zoom in to the desired level of detail.

For more information on BAM files please see the Working with BAM Files Tutorial, BAM file FAQ section, and Import BAMs video tutorial.

Current Windows and Mac OS Version is 3.9.1 (released January 8, 2024). Current Linux Version is 3.8.2 (released December 12, 2022).

Release Notes





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Last updated: 2019-09-26T19:39:39Z