VanLoo-lab ascat issues

VanLoo-lab / ascat

ASCAT R package

https://www.mdanderson.org/research/departments-labs-institutes/labs/van-loo-laboratory/resources.html#ASCAT

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issues

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Tumor_LogR, Tumor_BAF files with multiple tumor samples and single matched normal sample for use with ascat.asmultipcf()?

#181 agorelick opened 2 weeks ago
0
LogR correction, 10% overlap check

#180 maartenvanelst opened 1 month ago
0
Minor copy number is -1

#179 tbrendlerspaeth opened 1 month ago
1
How to choose input SNPs for ASCAT?

#178 bounlu closed 1 month ago
2
LogR calculation for tumor-only WES

#177 berguner closed 1 month ago
3
`ascat.runAscat` raw and ASCAT profile plots show different chromosome widths

#176 MikeWLloyd closed 2 months ago
2
Error in !is.null(homsegs) && !is.na(homsegs)

#175 duanshumeng closed 2 months ago
1
ASCAT could not find an optimal ploidy and purity value for sample logR.

#174 nandakumaryellapu closed 2 months ago
10
`ascat.runAscat` "vector size cannot be NA/NaN" and/or "subscript out of bounds"

#173 MikeWLloyd closed 2 months ago
2
ascat.prepareHTS ERROR in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, : line 1 did not have 4 elements

#172 tanayb001 closed 4 months ago
11
Error in function make_segments

#171 psuarezana closed 3 months ago
1
Confusion about GC and RT correction

#170 CHENAO-QIAN closed 5 months ago
2
Problem in createReplicTimingFile.R

#169 giorgiabiddau closed 4 months ago
2
Error when running on WES data

#168 CHENAO-QIAN closed 5 months ago
5
Error in NORMAL_COUNTS_tot

#167 bwubb closed 5 months ago
2
Error in !is.null(homsegs) && !is.na(homsegs) :

#166 mital14 closed 4 months ago
2
ASCAT could not find an optimal ploidy and purity value

#165 Coaxecva closed 4 months ago
3
No differences before and after LogR correction

#164 star0044 closed 7 months ago
2
Error in !is.null(homsegs) && !is.na(homsegs)

#163 wir963 closed 7 months ago
2
ASCAT could not find an optimal ploidy and purity value for sample

#162 mariaalexandrastanciu closed 9 months ago
6
Could not find optimal ploidy. Ploidy of 25.

#161 AngelGarciaDeLaTorreGarcia closed 8 months ago
3
Could not find optimal ploidy and purity

#160 albamasmalavila closed 9 months ago
2
Question regarding reference files

#159 teodorabu closed 10 months ago
1
Questions About WES

#158 WH-TEMP closed 10 months ago
1
Output query: Tissue samples have very high purity

#157 kane9530 closed 9 months ago
3
ascat output

#156 albamasmalavila closed 10 months ago
1
How to use ascat to call wes CNV

#155 lh12565 closed 10 months ago
2
Problem with ascat.prepareTargetedSeq

#154 h170607 closed 11 months ago
6
Adding Tumor-only mode for HTS (WGS) data

#153 jdemeul opened 1 year ago
1
Error in ascat.prepareHTS - alleleCounter version 4.3.0

#152 teodorabu closed 1 year ago
2
how to generate a LogR file for unmatched tumour sample

#151 esraa-jamal closed 11 months ago
2
Question about segments file: nmajor =0 and nminor>0

#150 kane9530 closed 1 year ago
3
Allele file

#149 jffpviana closed 1 year ago
2
ASCAT could not find an optimal ploidy and purity value for sample BEL_20C.

#148 chengwenxuan1997 closed 1 year ago
18
Jointly use sWGS and WES data

#147 WangKang-Leo closed 1 year ago
1
whether to remove duplicate reads

#146 chengwenxuan1997 closed 1 year ago
1
readAllelesFiles throws error

#145 liannesuurenbroek closed 1 year ago
3
Does the output of ASCAT use a 0-based or a 1-based coordinate system?

#144 xieduo7 closed 1 year ago
1
BED file for WES data

#143 mybabyfox closed 1 year ago
2
Warning with R 4.2.2

#142 kw10 closed 1 year ago
4
Install ASCAT 3.1.1 with conda

#141 ThibautMatis closed 1 year ago
1
ERRER with "ascat.prepareHTS"

#140 duanshumeng closed 1 year ago
16
Tumor-only mode

#139 suyanxun closed 1 year ago
1
How can I use ascat.prepareHTS to get the LogR and BAF file for tumor-only samples?

#138 suyanxun closed 1 year ago
1
Cosmetic change: use transparency in raw LogR and BAF plots to show data density

#137 jherrero closed 1 year ago
1
non-human genome

#136 gbnci closed 1 year ago
3
ascat.plotRawData picking up whole path, not filename

#135 anndalf closed 1 year ago
2
analyze the CNV of cancer cell lines with whole exome sequence

#134 LongpanUPC closed 1 year ago
4
Number of markers per segment

#133 kw10 closed 1 year ago
4
Loci and allele file missing for sex chromosomes WES (hg19 battenberg reference files)

#132 Indianhedgehog closed 1 year ago
2