QC failed for dataset provided for testing

[clodaghmcguire]

I've followed the steps to install visualMSI and the tried to testing the dataset provided.

visualmsi -i tumor.sorted.bam -r hg19.fasta -t msi.tsv

It loads the reference data, parses the tsv file the processes the provided tumour bam file; however, for each microsatellite location it says QC failed, zero reads (screenshot attached).

[hqu-arcus]

I have the same error, has this been solved? Thanks!

I solved this issue. I checked my reference GRCh37 and tsv file. The reference did not have chr notation in chromosome but my tsv file had every satellite specified with chr notation.