This method uses shallow Whole Genome Sequencing (sWGS) and the segmentation of a genomic profile to assess the Homologous Recombination Deficiency of a tumor based on the number of Large-scale Genomic Alterations (LGAs).
Hi,
I'm having a problem with shallowHRD for one of my samples while all the others worked.
/home/lom/anaconda3/bin/Rscript /home/lom/bin/softwares/shallowHRD/shallowHRD_hg19_controlfreec.R \
/mnt/diag/Analyses_NGS/2022/220210_NDX550301_RUO_0166_AHJVJTAFX3_PANEL_SOM_Shallow_R2_SV/ControlFreeC/output/2112L0012-A_S1.recal.bam_ratio.txt \
/mnt/diag/Analyses_NGS/2022/220210_NDX550301_RUO_0166_AHJVJTAFX3_PANEL_SOM_Shallow_R2_SV/ShallowHRD \
/home/lom/bin/softwares/shallowHRD/cytoband_adapted_hg19.csv
========================================================
Sample : 2112L0012-A_S1.recal
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Le chargement a nécessité le package : ggplot2
Warning message:
NAs introduits lors de la conversion automatique
on going...
The sample has been frozen like this all weekend and nothing is happening.
The only files created are:
Hi, I'm having a problem with shallowHRD for one of my samples while all the others worked.
The sample has been frozen like this all weekend and nothing is happening. The only files created are:
2112L0012-A_S1 recal_THR.jpeg
2112L0012-A_S1.recal_ratio_median_gathered.txt
Do you know what can block shallowHRD?
Thanks for your help
Flora