cancerit / CaVEMan

SNV expectation maximisation based mutation calling algorithm aimed at detecting somatic mutations in paired (tumour/normal) cancer samples. Supports both bam and cram format via htslib

http://cancerit.github.io/CaVEMan

cancerit/CaVEMan Issues

Error during mstep for whole exome sequencing data
Updated 5 months ago1
Continuous "core dumped" errors during the M step
Updated a year ago2
Caveman 1.14.0 Compilation error
Closed a year ago1
Implement.pm line 378 - species-assembly
Updated a year ago
Inquiry about the CaVEman option for running WGS data
Updated a year ago
Mstep - Error fetching reference sequence
Updated 2 years ago1
Error when executing split command
Closed 2 years ago2
Filtering fail "."
Updated 2 years ago
Merge - Warning
Updated 2 years ago
split step does not work correctly 1.13.15
Closed 2 years ago4
ignore region files
Updated 3 years ago
providing several samples for normal
Updated 3 years ago1
different tumor / normal platforms could be a warning instead of an error?
Updated 4 years ago
1.13.15: -x and -y parameters don't work in estep
Updated 4 years ago1
Error with caveman setup command
Closed 9 years ago3
VCF where ref == alt
Updated 5 years ago
what do these mean please
Closed 5 years ago1
1.13.9 - split error
Updated 5 years ago1
Output for every site?
Closed 5 years ago2
1.13.5 - Segmentation fault (core dumped) - Estep
Closed 5 years ago1
estep issue with version 1.13.3 . - fai_access Error
Closed 6 years ago3
1.13.5 - mstep errors - negative positions
Updated 6 years ago
caveman estep 1.12.0
Closed 6 years ago12
Installation problem - CaVEMan 1.7.5
Closed 6 years ago2
Pre-release tag overlapping_reads
Closed 6 years ago3
estep help for options -l and -r
Closed 6 years ago1
bam_access_get_avg_readlength_from_bam: doesn't filter out sec/supp reads
Closed 6 years ago
split.c - cli options parsed but never used
Closed 6 years ago2
Split bug (sparse data edge-case)
Closed 6 years ago3
error in caveman estep 1.12.0
Closed 7 years ago11
mstep - covs arrays could be optimised to reduce I/O for little CPU cost
Closed 7 years ago
Fast gzip compress estep snps/muts VCFs to reduce I/O & tmp footprint
Closed 7 years ago3
mergeCavemanResults
Closed 7 years ago8
Fail to parse output VCF files due to invalid UTF-8
Closed 7 years ago3
caveman mstep with error: split_access_get_section_from_indexv Error opening split list file.
Closed 7 years ago2
CAVEMAN: Somatic Calls in SNPs File
Closed 7 years ago2
Error opening file to read cov array
Closed 7 years ago2
Incorrect genotype sorting in SNP calls
Updated 7 years ago
ERROR of esteps in 1.10.0
Closed 8 years ago2
any best practices for RNA-seq SNV calling?
Closed 8 years ago1
can --ignore-regions-file flag be used to ignore all but the chromosome of interest?
Closed 8 years ago3
Unmatched platforms result in an error but not an exit.
Closed 8 years ago2
specifying external htslib
Closed 8 years ago
no calls gives unusual file sets
Updated 9 years ago2
check BAM headers in setup for readgroups
Closed 9 years ago1
generateCavemanUMNormVCF - get sample names from BAM header
Updated 9 years ago
generateCavemanUMNormVCF - Unmatched VCF generation errors
Closed 9 years ago
Copy number file defaults
Closed 9 years ago
High number of lanes causes error in merge
Closed 9 years ago
Crash when encountering a "bad" read
Closed 9 years ago8