Test IGV for alignment visualisation

[sebschulz1]

Integrated Genome Viewer (IGV) was suggested previously as a visualisation tool.

• It needs to be discussed what it would take to integrate it and if it does provide substantial advantages over Sabre
• Sanger trace electropherograms cannot be visualised in IGV
• One advantage could be that genetic element annotations can be visualised by uploading an annotation file (e.g. gtf)

Goal is to test out its functionality using output files from the sangerseq tool.

[sebschulz1]

Preliminary assessment of IGV for visualising tracy output files:

• ab1 files: Sanger chromatograms cannot be visualised in IGV (as expected)
• Variant calling files: bcf files can be easily converted into vcf using bcftools. vcf files are then loaded into IGV and can be viewed along with a reference fasta file
• Annotation files: GenBank files are not accepted by IGV. Instead, gtf or gff files need to be provided for annotation
• Alignment files: .align or align.fa files from tracy cannot be visualised in IGV; instead SAM or BAM files would need to be provided