Barcodes pileup_and_phase

[petrsh]

Hi @teng-gao ,
thanks for developing this nice tool! I'm currently testing it and comparing it with the Copykat and inferCNV and unexpectedly getting bad results and weird errors for some samples. Before posting their description here, I wanted to check if one should use only barcodes for high-quality cells (i.e. after QC and doublet removal) during the pileup_and_phase step? I used all barcodes from the barcodes.tsv files from the filtered_feature_bc_matrix folders .... could this cause the issues?

[teng-gao]

Hi @petrsh,

That shouldn't cause issues. Could you describe the problems? Pasting some bulk HMM profiles would be most helpful.