Genomecomb moved to github on https://github.com/derijkp/genomecomb with documentation on https://derijkp.github.io/genomecomb. For up to date versions, go there. These pages only remain here for the data on the older scientific application (or if someone really needs a long obsolete version of the software)

Howto view results

This text gives examples of how to view results in a projectdir using the gui cg viz.

In the howto, the smal example and test data set ori_mixed_yri_mx2 downloadable from the genomecomb website will be used. This data set was derived from publically available exome and genome sequencing data by extracting only raw data covering the region of the MX2 gene (on chr21) and a part of the ACO2 gene (on chr22).

This howto expects a processed projectdir in tmp/mixed_yri_mx2. This can be created following the directions in howto_process_project. Alternatively you could also copy it from the expected dir (or adapt the path):

    cp -a expected/mixed_yri_mx2 tmp/mixed_yri_mx2

Startup

Start up cg viz using

cg viz tmp/mixed_yri_mx2/compar/annot_compar-mixed_yri_mx2.tsv.lz4

This opens the annotated combined variant file (fomrmat described in tsv) using cg viz, allowing you to browse through the table (even if it is millions of lines long).

Fields

You can use the Fields button to limit the number of fields you want to see. The list on the right of the dialog shows the currently displayed fields. The list on the left shows available fields. Sample specific fields are indicated by having a - followed by a sample suffix. We will select to display only a limited set of sample specific fields:

Click "Fields"
Filter all sample specific fields in the right list by typing a - in the Filter field above it
Use the left button (<-) to remove all these fields from display (right list)
Delete the - in the filter to show the remaining fields again
Click on the "alt" field; we will add back some of the sample fields after this field
In the "Filter" field in the left selection box, enter "^zyg|^qual"; only fields starting with "zyg" or "qual" will be shown
Use the right arrow button (->) to add them to the display
You may also add or remove fields by selecting them with the mouse, and using the "<-" or "->" button
Click "Go" Now only the selected fields are displayed. Longer field names in the title line are cut off; make these visible by selecting the line between title and table, and drag it lower.

The sample fields have a specific format, e.g.

zyg-gatk-rdsbwa-exNA19240mx2: indicates the zygosity (as described in tsv) for this variant by the gatk variant caller on the reads aligned using bwa of the sample exNA19240mx2.
zyg-sam-rdsbwa-exNA19240mx2: contains the zygosity according to the sam variant caller for the same sequence sample.
zyg-gatk-rdsbwa-gilNA19240mx2: The same biological sample (NA19240) was also genome sequenced, and sequence sample gilNA19240mx2 contains this data. zyg-gatk-rdsbwa-gilNA19240mx2 is then the zygosity called using the same analysis tools on the genome sequence sample.

When combining sample results, process_project will check if a variant is not present in a sample variant list, whether this is due to actually being reference (zyg = r) or being unsequenced (zyg = u), according to the criteria used. also other data, such as the quality of the "variant" call, is added for the reference calls where possible. You can see that no quality value is available (quality-* = ?) for unsequenced variants (zyg-* = u)

Query

You can use Query to show only lines that fit a number of criteria. The query language is the same as supported by cg select and the specifics can be found in the cg select help. You can type a query directly into the Query field at the top, e.g. type $zyg-gatk-rdsbwa-gilNA19240mx2 == "m" to select only variants that are homozygous gatk calls for sample gilNA19240mx2 and press Enter.

You can use the "Query" button to get help in building queries or the "EasyQuery" button for adding some common queries in an easier way.

Summaries

The Summaries button can be used to create summary data. This provides functionality similar to the -g and -gc options in cg select (more info in the cg select help), but you can select fields etc. in the GUI.

For example:

Click Summaries
Select "chromosome" in the fields column (left)
Click "Add to row grouping" (top right)
Click "Summary" button at the bottom
The number of variants per chromosome is shown
Clear the query and press Enter to change to a summary of the full data set
Select "data" in the Selection button next to the Summaries button to return to the normal data view

Tree view

Make the tree view on the left larger by dragging the dividing line to the right. Here you can select other result files to view.

Click on reports directory in compar. This contains combined reports data. Individual (more extensive) reports are in the sampledirs.
Select report_stats-mixed_yri_mx2.tsv
Enter $parameter eq "fw_numreads" as a query
See the number of reads in the fastq files for each sample (that started from fastq files)

Home

Contact

Installation