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hepcat72
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vcfSampleCompare
Filter and rank variant call files (VCF) based on comparative evidence ratios between groups of samples.
GNU General Public License v3.0
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Add errors about missing required input format components
#27
hepcat72
opened
3 years ago
0
VcfSampleCompare - empty output with warnings
#26
nevosmic
opened
3 years ago
8
Help with vcf format
#25
IsabelFE
closed
3 years ago
2
Add pair IDs to the file header
#24
hepcat72
opened
4 years ago
0
Files merged via `bcftools merge` can result in errors
#23
hepcat72
closed
4 years ago
1
Add an overall weighted score
#22
hepcat72
opened
5 years ago
0
Add a pair summary at the top of the output in a comment section
#21
hepcat72
closed
5 years ago
7
Implement weighted score/sorting
#20
hepcat72
closed
5 years ago
0
Weighted scores for sorting instead of sub-sorting
#19
hepcat72
closed
5 years ago
5
Allow sample groups to be supplied using column numbers
#18
hepcat72
opened
5 years ago
4
Add tests
#17
hepcat72
closed
5 years ago
0
Handle the missing data case better
#16
hepcat72
closed
5 years ago
1
Handle the case where all obs rats are the same between the 2 groups
#15
hepcat72
closed
5 years ago
3
Order the samples in each sample group based on the original order in the vcf file header
#14
hepcat72
closed
5 years ago
0
Account for low depth
#13
hepcat72
closed
5 years ago
1
Add a "penalize depths below" option
#12
hepcat72
closed
5 years ago
0
Make the sub-sort be on allelic frequency instead of average depth
#11
hepcat72
closed
5 years ago
8
Base the score in genotype mode on the ratio of resolution
#10
hepcat72
closed
5 years ago
2
Base the separation gap on max/min difference instead of the difference in the averages
#9
hepcat72
closed
5 years ago
4
Make pair identifier unique for groupings when -s not provided
#8
hepcat72
closed
5 years ago
4
Add algorithm description for sorting & filtering
#7
hepcat72
closed
5 years ago
0
Set a filter and score value in VCF instead of filtering & sorting
#6
hepcat72
opened
5 years ago
0
Add ploidy option
#5
hepcat72
opened
5 years ago
0
Version 2.0 Changes
#4
hepcat72
closed
6 years ago
1
Issue error if bad sample names supplied to -s
#3
hepcat72
closed
6 years ago
1
If there's only 1 sample, requiring hits<1 makes no sense
#2
hepcat72
closed
6 years ago
1
Add a ratio min difference parameter
#1
hepcat72
closed
6 years ago
1