KChen-lab Monopogen issues

KChen-lab / Monopogen

SNV calling from single cell sequencing

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issues

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Can i run Monopogen for non-tumor sample?

#67 ZehangJiang opened 1 day ago
0
can the somatic module identify indels?

#66 ad2n15 closed 1 week ago
3
germ line module not detecting full chromosome

#65 aidanshoham12 opened 2 weeks ago
3
Somatic Module on multiple chromosomes

#64 Arsamat opened 1 month ago
0
openCRAVAT application

#63 ariannadib opened 1 month ago
2
bam.lst file format

#62 aidanshoham12 opened 1 month ago
1
Error during LDrefinement

#61 Thapeachydude opened 1 month ago
9
The error in Germline calling step

#60 zhangdong360 closed 1 month ago
3
cell_snv.mat.gz missing

#59 ariannadib closed 1 month ago
8
Different somatic calls across Monopogen v.1.0 and v1.6.0

#58 ypershad opened 2 months ago
5
Cell by SNV matrix for germline

#57 yunguan-wang closed 1 month ago
1
v1.5.0 Monopogen fails on example data in "Somatic SNV calling from scRNA-seq"

#56 briansha closed 1 month ago
4
Missing chr20.germline.vcf from germline calling step

#55 briansha opened 2 months ago
8
Error in Germline SNV calling

#54 Teerapon789 opened 2 months ago
5
outputs of cellScan

#53 ariannadib opened 2 months ago
3
Error in ld refinement on putative somatic SNVs

#52 zhangdong360 closed 1 month ago
3
region "-o" specifies an unknown reference name

#51 ariannadib opened 2 months ago
1
chr20.gp.vcf.gz: No such file or directory

#50 dipingxian431 opened 3 months ago
5
number of snps before and after first out of imputation prior to phasing

#49 tbrunetti closed 3 months ago
2
GermCalling Target Markers

#48 ArunaNannapaneni closed 1 month ago
9
Germline job never finish

#47 MetteBoge opened 3 months ago
12
fixed

#46 MetteBoge closed 3 months ago
0
Lineage tracing

#45 SofiaFreiman closed 1 month ago
1
Monopogen’s test object

#44 dzxiaona closed 4 months ago
1
Run monopogen for more than 1 sample?

#43 ZhengJIN94 closed 1 month ago
2
Updates to Monopogen to work with new versions of samtools + bcftools

#42 swvanderlaan opened 4 months ago
0
region-file

#41 swvanderlaan closed 4 months ago
2
Explanation .gl, .gp, .phased files

#40 rafaella-buzatu opened 4 months ago
1
Can Monopogen use for calling variants in Malaria parasite single cell Data ?

#39 MJBioInfo closed 4 months ago
3
Bulk RNA seq

#38 ArunaNannapaneni closed 4 months ago
1
Imprinted genes identification

#37 singcell closed 5 months ago
2
Issues for germline variant calling part from scRNA-seq

#36 lijinw closed 1 month ago
3
about cell counts in somatic SNV output(chr*.putativeSNVs.csv)

#35 hanjun98 opened 5 months ago
2
Missing genotypes？

#34 wangjunyu-cumt opened 5 months ago
7
Whether SmartSeq data can be used with the Somatic function？

#33 zuoyichen closed 5 months ago
3
Requires unsupported openssl version

#32 ArunaNannapaneni opened 6 months ago
0
Error in Germline

#31 parth2608 opened 6 months ago
3
Issues in the test file chr20.maester_scRNA.bam for somatic mutation calling

#30 alextidd opened 7 months ago
7
Installation error

#29 swvanderlaan closed 5 months ago
1
Fixing minor typos

#28 seb951 closed 2 months ago
0
Error on somatic calling

#27 solarkang21 closed 7 months ago
1
Error on gemline calling

#26 carolwxm opened 8 months ago
1
About Error for the cellScan step during Somatic Variant Calling

#25 neuroniko closed 5 months ago
2
preprocess error

#24 zheng-sc opened 8 months ago
2
Tutorial Somatic Variant Calling Error for the cellScan step. Different output for different input to -t and -w? Potentially different reference file?

#23 hannahkimincompbio closed 1 month ago
2
Monopogen for mouse single cell sequence

#22 Lixinyoung closed 1 month ago
1
nothing in the germline.vcf file

#21 hanliu0119 opened 9 months ago
2
missing a space between flag and file name

#20 fulabgenomics closed 9 months ago
3
fix bug on str to int on -k is float

#19 monoplasty closed 9 months ago
0
About ld refinement on putative somatic SNVs, spend a lot of time

#18 monoplasty opened 9 months ago
3