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Issues list

Combining multiple runs of pileup_and_phase script
#125 opened May 22, 2023 by ms3389
4
snp_index must be size 0 or 1, not 2 [pileup_and_phase.R] enhancement New feature or request
#47 opened Oct 11, 2022 by jgarces02
@teng-gao
21
Error in filter() when calling run_numbat
#51 opened Nov 1, 2022 by aseyedia
4
Error in if (UPGMA_score > NJ_score) bug Something isn't working
#68 opened Nov 28, 2022 by teng-gao
12
[W::bam_hdr_read] bgzf_check_EOF: No such file or directory
#76 opened Dec 7, 2022 by yintz
1
Problem with pileup_and_phase; cM values NaN for all chromosomes but Chr1 and Chr2
#78 opened Dec 9, 2022 by dejonggr
2
Running numbat failed on large datasets: cannot allocate memory block of size 134217728 Tb
#83 opened Dec 26, 2022 by JikaiShao
3
High-clonality CNVs not called
#84 opened Dec 27, 2022 by teng-gao
Expecting loss but getting CNLoH
#93 opened Jan 12, 2023 by tinakeshav
6
Parameter finetuning for cell line
#99 opened Jan 27, 2023 by aranham
Settings for running on large number of cells
#104 opened Feb 14, 2023 by aranham
4
error in unused argument when running pileup_and_phase.R
#114 opened Apr 19, 2023 by MigleMi
1
Account for WGD enhancement New feature or request
#36 opened May 30, 2022 by teng-gao
3
Error Running HMMs running Numbat
#121 opened May 11, 2023 by lopezCascales
1
Error with SNP contamination for some samples
#127 opened May 26, 2023 by Sarah145
2
run_numbat() gives error: running hclust...Error in vectbl_assign(x[[j]], i, recycled_value[[j]])
#128 opened May 28, 2023 by kzb193
2
Phylogeny on merged samples
#130 opened Jun 23, 2023 by freddie090
6
How to re-run from the breakpoint enhancement New feature or request
#131 opened Jun 29, 2023 by daisyyr
3
memuse is not installed by default - breaking your script
#132 opened Jun 30, 2023 by stela2502
1
how to specify the number of clones in the bulk_clones_final.png and look at the allele frequency profile based on the specified number of clones
#133 opened Jul 11, 2023 by rosaranli
8
Target and ref have too few matching SNPs [pileup_and_phase.R]
#136 opened Sep 5, 2023 by Franzili
2
Error in hclust(dist_mat, method = "ward.D2") : size cannot be NA nor exceed 65536
#137 opened Sep 13, 2023 by YiweiNiu
Error in run_numbat (dpoilog: all x must be integers)
#138 opened Sep 14, 2023 by RaghadShu
4
No SNPs left
#140 opened Sep 15, 2023 by moOsmanMD
1
Comparison to pseudobulk and sanity check of high major copy number documentation Improvements or additions to documentation
#194 opened Jul 1, 2024 by Nikki-Burdett
6
ProTip! Adding no:label will show everything without a label.