iqbal-lab-org minos issues

iqbal-lab-org / minos

Variant call adjudication

MIT License

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issues

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bug fix --filter_min_frs should be float

#124 martinghunt closed 3 months ago
0
no loop devices available

#123 dpenas-u closed 1 year ago
3
Update gramtools

#122 martinghunt closed 1 year ago
0
Gramtools ee98085fbb9d8be5afd2288424c3d6dded796ab8

#121 martinghunt closed 1 year ago
0
Variants at contig ends

#120 martinghunt closed 1 year ago
0
Compatibility issues between minos' gramtools.py script and gramtools' command

#119 ycode-sh closed 1 year ago
41
Add test data

#118 martinghunt closed 2 years ago
0
Ignore all non-ACGT alleles from input VCF files

#117 martinghunt closed 2 years ago
1
How to build a manifest.tsv file. Can you provide a sample file?

#116 joybio opened 2 years ago
18
i don't know error

#115 kdyoung100 opened 2 years ago
4
GitHub actions instead of travis

#114 martinghunt closed 2 years ago
0
Fixed #112. Added libjpeg-dev to dependencies

#113 jordivea-odap closed 2 years ago
0
Missing jpeg library when building the Singularity image

#112 jordivea-odap closed 2 years ago
0
Depth tags and filter fixes

#111 martinghunt closed 3 years ago
0
Install for minos is broken gramtools dependency issue

#110 annacprice closed 3 years ago
2
Negative binomial fixes

#109 martinghunt closed 3 years ago
0
Fixes to handle when non-ACGT is in ref fasta

#108 martinghunt closed 3 years ago
0
Add opt to make distance matrix at end of regeno pipeline

#107 martinghunt closed 3 years ago
0
Regeno filter samples

#106 martinghunt closed 4 years ago
0
Regeno improvements

#105 martinghunt closed 4 years ago
0
Genotyping distributions fixes

#104 martinghunt closed 4 years ago
0
Remove precision and recall code. No longer used

#103 martinghunt closed 4 years ago
0
Change default VCF filters

#102 martinghunt closed 4 years ago
0
Default homozygous calling

#101 martinghunt closed 4 years ago
0
Write contig header lines to final vcf

#100 martinghunt closed 4 years ago
0
Add contig header lines to final.vcf

#99 martinghunt closed 2 years ago
0
Dump binary encoded genotypes after regenotyping

#98 iqbal-lab opened 4 years ago
3
Disable plots made by minos adjudicate

#97 martinghunt closed 4 years ago
0
Genotyping refactoring and fix diploid coverage collection

#96 bricoletc closed 4 years ago
0
multi sample pipeline is broken if not splitting the VCFs

#95 martinghunt closed 4 years ago
0
Do not cluster adjacent variants

#94 martinghunt closed 4 years ago
0
Add travis and singularity

#93 martinghunt closed 4 years ago
2
Call filtering

#92 martinghunt closed 4 years ago
0
Update gramtools

#91 martinghunt closed 4 years ago
0
Ignore bad vcf pos

#90 martinghunt closed 4 years ago
0
Vcf fixes

#89 martinghunt closed 4 years ago
0
Stop if too many variants

#88 martinghunt closed 4 years ago
0
Speed up genotyping

#87 martinghunt closed 4 years ago
0
Speed up genotyping

#86 martinghunt closed 4 years ago
0
Update to use latest gramtools commit 958fd53a4198835a99de5d0ae24399e…

#85 martinghunt closed 4 years ago
0
Try to make valid VCF file

#84 martinghunt closed 4 years ago
1
General tidying up

#83 martinghunt closed 4 years ago
0
Add singularity container file

#82 martinghunt closed 4 years ago
1
Use entry points

#81 martinghunt closed 4 years ago
1
Make unit tests discoverable

#80 martinghunt closed 4 years ago
2
Math error during genotyping

#79 bricoletc closed 5 years ago
0
Null genotypes missing GT_CONF_PERCENTILE value

#78 mbhall88 closed 5 years ago
6
Invalid DP FORMAT header

#77 mbhall88 closed 4 years ago
5
removing perl_generated_vcf caused a bug

#76 iqbal-lab closed 5 years ago
3
nextflow script for multisample does not respect cached precluster_small_vars_merge

#75 iqbal-lab closed 4 years ago
8