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sample name is taken from file, not the bams list, if samples are named different, but all files in different folders named atac_fragments.bam, then you will get one "sample" variants titled "atac_fragments"

Status: Open.

#127 In KChen-lab/Monopogen;

· mjesse-github opened on Jul 23, 2026

broken binaries in apps/ and thus failed vcf files using the germline module

Status: Open.

#126 In KChen-lab/Monopogen;

· mjesse-github opened on Jul 21, 2026

Inquiry regarding UMI deduplication and PCR bias mitigation for ASE analysis

Status: Open.

#125 In KChen-lab/Monopogen;

· Arsenalwins opened on Dec 14, 2025

Tutorial on scATAC-seq SNP calling?

Status: Open.

#124 In KChen-lab/Monopogen;

· Luosanj opened on Nov 17, 2025

samtools: Permission denied

Status: Open.

#123 In KChen-lab/Monopogen;

· parvathisudha opened on Oct 16, 2025

how to make CB_7K.maester_scRNA.csv

Status: Open.

#122 In KChen-lab/Monopogen;

· Arsenalwins opened on Aug 11, 2025

mut_mat in LDrefinement.R

Status: Open.

#121 In KChen-lab/Monopogen;

· yt723 opened on Jul 30, 2025

Question about somatic step: handling multi-sample input, -s option, and duplicated barcodes

Status: Open.

#120 In KChen-lab/Monopogen;

· ttt-404 opened on Jul 22, 2025

cellScan step in vignette takes too long to complete

Status: Open.

#119 In KChen-lab/Monopogen;

· tomasnoli opened on Jul 8, 2025

ValueError in cellScan: "Unstacked DataFrame is too big, causing int32 overflow"

Status: Open.

#118 In KChen-lab/Monopogen;

· lhy329 opened on Jul 7, 2025

Germline analysis

Status: Open.

#117 In KChen-lab/Monopogen;

· tkcaccia opened on Jul 3, 2025

ID1 vs ID2 in bam.lst and biological donor knowledge?

Status: Open.

#115 In KChen-lab/Monopogen;

· mkarikom opened on Apr 22, 2025