Ecosyste.ms: Issues

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GitHub / TRON-Bioinformatics/vafator issues and pull requests

#46 - Maximum depth threshold?

Issue - State: open - Opened by sejmodha over 1 year ago

#45 - Does this have support for cram files?

Issue - State: open - Opened by smk5g5 over 1 year ago

#44 - Add ambiguous bases annotations

Pull Request - State: closed - Opened by priesgo about 2 years ago - 2 comments

#43 - VAFATOR doesn't assign VAF to a well know Trinucleotide-Bloc Mutation

Issue - State: closed - Opened by Rohit-Satyam about 2 years ago - 5 comments

#42 - The DP field counts doesn't match with counts in IGV

Issue - State: closed - Opened by Rohit-Satyam about 2 years ago - 5 comments

#41 - Fix CN less one

Pull Request - State: closed - Opened by priesgo about 2 years ago

#40 - Expected allele frequency is > 1 for some mutations

Issue - State: closed - Opened by lbresadola about 2 years ago - 2 comments
Labels: bug

#38 - Bugfix non query position

Pull Request - State: closed - Opened by priesgo over 2 years ago

#36 - fix wrong annotation names + fix the annotation types

Pull Request - State: closed - Opened by priesgo over 2 years ago

#35 - BED file with local purities not properly recorded in VCF header

Issue - State: open - Opened by priesgo over 2 years ago
Labels: bug

#34 - update dependencies to have more flexibility

Pull Request - State: closed - Opened by priesgo over 2 years ago

#33 - 29 rank sum test

Pull Request - State: closed - Opened by priesgo over 2 years ago

#32 - Absolute power second go

Pull Request - State: closed - Opened by priesgo over 2 years ago

#31 - Absolute power implementation

Pull Request - State: closed - Opened by priesgo over 2 years ago

#30 - Improve power calculation to absolute method

Issue - State: closed - Opened by priesgo over 2 years ago - 1 comment

#28 - Add some additional metrics for MQ, BQ and position within read

Pull Request - State: closed - Opened by priesgo over 2 years ago

#27 - Implements the power to call a mutation

Pull Request - State: closed - Opened by priesgo over 2 years ago

#26 - fix command line conflicting argument

Pull Request - State: closed - Opened by priesgo over 2 years ago

#25 - Update vafator2decifer script with filter by purity and other goodies

Pull Request - State: closed - Opened by priesgo over 2 years ago

#24 - Fix nf mq thr

Pull Request - State: closed - Opened by priesgo almost 3 years ago

#23 - When DP=0 avoid adding VAF=0.0

Issue - State: open - Opened by priesgo almost 3 years ago

#22 - Bugfix DP indels

Pull Request - State: closed - Opened by priesgo almost 3 years ago

#21 - Improve performance

Pull Request - State: closed - Opened by priesgo almost 3 years ago

#20 - 19 bug order bams

Pull Request - State: closed - Opened by priesgo almost 3 years ago

#19 - When passing multiple BAM with --bam the order change the results unpredictably!

Issue - State: closed - Opened by priesgo almost 3 years ago - 1 comment
Labels: bug

#18 - Header line in output VCF contains name of input/output VCF instead of path

Issue - State: closed - Opened by priesgo almost 3 years ago
Labels: bug

#17 - add support in vafator for better input

Pull Request - State: closed - Opened by priesgo about 3 years ago

#16 - fix issue with MNVs + ensure workflow tests work

Pull Request - State: closed - Opened by priesgo about 3 years ago

#15 - Fix issue when --bam is not provided + add automated integration tests

Pull Request - State: closed - Opened by priesgo about 3 years ago

#14 - Vafator2decifer

Pull Request - State: closed - Opened by priesgo about 3 years ago

#13 - Support indels

Pull Request - State: closed - Opened by priesgo about 3 years ago - 1 comment

#12 - change conda environment name to vafator

Pull Request - State: closed - Opened by priesgo about 3 years ago

#11 - fix issue on swapped tumor and normal BAMs

Pull Request - State: closed - Opened by priesgo about 3 years ago

#10 - fix issue on nextflow workflow

Pull Request - State: closed - Opened by priesgo about 3 years ago

#9 - Add support for indels

Issue - State: closed - Opened by priesgo about 3 years ago - 1 comment
Labels: high priority

#8 - Add summary stats of the BQ of supporting reads

Issue - State: closed - Opened by priesgo about 3 years ago - 1 comment

#7 - Add summary stats on the MQ of supporting reads

Issue - State: closed - Opened by priesgo about 3 years ago - 1 comment

#6 - Add annotation on the unique mapping of reads

Issue - State: open - Opened by priesgo about 3 years ago

#5 - Add average edit distance annotation

Issue - State: open - Opened by priesgo about 3 years ago

#4 - Add clustered position within the read annotations

Issue - State: open - Opened by priesgo about 3 years ago

#3 - Add strand bias annotations

Issue - State: open - Opened by priesgo about 3 years ago
Labels: high priority

#2 - Add --prefix + migrate to Nextflow DSL2

Pull Request - State: closed - Opened by priesgo about 3 years ago

#1 - Makes Nextflow workflow work with conda + add automated tests

Pull Request - State: closed - Opened by priesgo about 3 years ago