Giters
iqbal-lab-org
/
minos
Variant call adjudication
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16
Watchers:
4
Issues:
44
Forks:
5
iqbal-lab-org/minos Issues
no loop devices available
Closed
a year ago
Comments count
3
Compatibility issues between minos' gramtools.py script and gramtools' command
Closed
a year ago
Comments count
41
How to build a manifest.tsv file. Can you provide a sample file?
Updated
2 years ago
Comments count
18
Check if whitespace in seq names breaks minos
Closed
2 years ago
Comments count
2
Add contig header lines to final.vcf
Closed
2 years ago
i don't know error
Updated
2 years ago
Comments count
4
Ignore all non-ACGT alleles from input VCF files
Closed
2 years ago
Comments count
1
Missing jpeg library when building the Singularity image
Closed
3 years ago
Install for minos is broken gramtools dependency issue
Closed
3 years ago
Comments count
2
multi sample pipeline: ALT allele list in final VCF differ between samples/files
Closed
4 years ago
Comments count
7
hardcoded ram limit for one step of multisample workflow
Closed
4 years ago
nextflow script for multisample does not respect cached precluster_small_vars_merge
Closed
4 years ago
Comments count
8
Stop if too many variants
Closed
4 years ago
multi sample pipeline is broken if not splitting the VCFs
Closed
4 years ago
Dump binary encoded genotypes after regenotyping
Updated
4 years ago
Comments count
3
Invalid DP FORMAT header
Closed
4 years ago
Comments count
5
add travis
Closed
4 years ago
Make unit tests discoverable
Closed
4 years ago
Comments count
2
Add singularity container file
Closed
4 years ago
Comments count
1
Try to make valid VCF file
Closed
4 years ago
Comments count
1
Use entry points
Closed
5 years ago
Comments count
1
Null genotypes missing GT_CONF_PERCENTILE value
Closed
5 years ago
Comments count
6
Math error during genotyping
Closed
5 years ago
removing perl_generated_vcf caused a bug
Closed
5 years ago
Comments count
3
multi-sample pipeline: parallelise (nextflow) chunk building
Closed
5 years ago
Comments count
3
Option to not use unmapped reads in multi sample pipeline
Closed
5 years ago
Comments count
2
Filter on depth and gt conf percentile
Closed
5 years ago
Comments count
4
gramtools quasimap `--run-directory` deprecated
Closed
6 years ago
multi sample pipeline keep zero cov alleles
Closed
6 years ago
Implement multithreading gramtools build vcf chunks
Closed
6 years ago
remove cortex MISMAPPED_UNPLACEABLE VCF records
Updated
6 years ago
Comments count
1
if chunking VCF, check bam is indexed
Updated
6 years ago
multi_sample_pipeline limit max alleles
Closed
6 years ago
multi_sample_pipeline --norun FileNotFoundError
Closed
6 years ago
Logging issues
Closed
6 years ago
Remove alleles that are not seen from final VCF
Closed
6 years ago
Implement chunking the reference genome
Closed
6 years ago
Comments count
2
Add support for large variant calls in multi-sample pipeline
Updated
6 years ago
rigorous checking of gramtools quasimap success/fail
Closed
6 years ago
handle no variants in input VCF
Closed
6 years ago
no genotype call when no read cov
Closed
6 years ago
Comments count
1
More logging info
Closed
6 years ago
Catch when gramtools fails
Closed
6 years ago
Comments count
1
allow >1 reads file as input
Closed
6 years ago