Sen ZHAO

icon indicating an email [email protected]

icon company Oslo University Hospital icon location Montebello, N-0379 Oslo, Norway icon location Bioinformatics, -omic data, cancer research

Results 3 comments of Sen ZHAO

share idea of fusion "biomarker_mapping"

Hi @1seokyoo, I agree with Sigve @sigven that fusion breakpoint coordinate available in CIVic is not in a good resolution. If you think about to include the fusion breakpoint in...

Pipeline does not complete variant calling when staring from the '--step prepare_recalibration'

config file: [markduplicate.txt](https://github.com/nf-core/sarek/files/9664402/markduplicate.txt) input file: [markduplicates_no_table.csv](https://github.com/nf-core/sarek/files/9664406/markduplicates_no_table.csv) As the bam files (after MarkDuplicates) in the input sheet are private, I could not share with you now. Could you replace them with...

Pipeline does not complete variant calling when staring from the '--step prepare_recalibration'

BTW, in the output directory, no 'preprocessing' folder (which saves *.recal.bam) is available. I also screen the intermediate directory 'work' - there was *.recal.bam file of each genomic interval (recalibration...