run-marker-blast-annotation-illumina.md

Run Marker BLAST Annotation

BLAST (Basic Local Alignment Search Tool) determines if markers are useful by aligning the probe sequences to the genome. A marker is not useful if it aligns to multiple locations on a genome.

BLAST will run on the marker positions in markerPositions.txt.

1: Parse Sample Files step [parse-samples] must have been run already or must be selected

This step uses the sampRAF files that were created in the Parse Sample Files step.

2: Word size (length of the smallest continuous match reported)

[1-100, default 40; number of base pairs?; talk to John Lane] Smaller word size-->more time to run Markers are 50 bp in length Checking is subunits of the marker have matches in the sample genome?

3: Full path to an Illumina manifest file (e.g., HumanExome-12-v1-o-B.csv)

You must provide a manifest with probe sequences.

4: (optional) Marker positions file to override MarkerSet positions with (e.g. for a different genome build) (e.g. markerPositions.txt)

Use this option if you want to BLAST on a different genome build than that of your project. For example, if the project was created in hg37 and the positions in markerPositions.txt are hg37, you can provide an alternative markerPositions file with positions in hg38 for this part.

5: Number of threads

6: Download remotely available BLAST program requirement

Genvisis will download this program automatically when you check the Run Marker BLAST Annotation step. [VERIFY WITH ROSE]