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tfwillems
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HipSTR
Genotype and phase short tandem repeats using Illumina whole-genome sequencing data
GNU General Public License v2.0
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Add per-sample filtering explanations
#48
nh13
closed
6 years ago
1
Add the --min-qual-sum-log-prob option to control how reads are filtered
#47
nh13
opened
6 years ago
0
Stutter model failed to converge at a site
#46
nh13
closed
6 years ago
5
Genotyping locus failed due to MAX_STUTTER_REPEAT_DEL (no explanation in the log)
#45
nh13
closed
6 years ago
2
Compatibility with .bam from 10x Genomics
#44
stephenwilliams22
closed
6 years ago
11
No GL output in Model 1
#43
shukwong
closed
6 years ago
2
compiling htslib in release 0.5
#42
shukwong
closed
6 years ago
2
All input reads filtered as "did not have a unique mapping"
#41
npilshchikova
closed
6 years ago
2
Building using releases
#40
cking-ha
closed
7 years ago
1
ERROR: BAM header mismatch issue
#39
npatel22526
closed
7 years ago
5
Question: FLANK_ASSEMBLY_CYCLIC
#38
nh13
closed
6 years ago
4
Filter scripts should align the last line of the stats file
#37
nh13
closed
7 years ago
0
Contigs missing in output VCF
#36
nh13
closed
7 years ago
2
Best way to debug when the stutter model fails to train?
#35
nh13
closed
6 years ago
4
HipSTR uses bases from overlapping read pairs
#34
nh13
closed
7 years ago
1
Filter out reads that do not span an STR region
#33
nh13
closed
7 years ago
5
Compilation on Windows
#32
nh13
closed
6 years ago
1
Genotype FORMAT tags should have a proper type
#31
nh13
closed
7 years ago
5
Control the maximum # of flanking sequences via the command line.
#30
nh13
closed
7 years ago
7
Fix a typo
#29
nh13
closed
7 years ago
0
Question: can HipSTR output confident reference calls?
#28
nh13
closed
7 years ago
1
Missing genotypes for some variants
#27
nh13
closed
7 years ago
2
Output VCF is not sorted by coordinate
#26
nh13
closed
7 years ago
1
handle errors from htslib
#25
brentp
closed
6 years ago
5
CRAM reading is too slow
#24
tfwillems
closed
7 years ago
1
--quiet option ?
#23
brentp
closed
7 years ago
5
Fix or read name clashes across filenames
#22
mgymrek
closed
7 years ago
1
Limit number of flanking haplotypes.
#21
tyjo
closed
7 years ago
0
Check for PyVCF installation within filtering scripts
#20
tfwillems
closed
7 years ago
3
Add CRAM support
#19
tfwillems
closed
7 years ago
0
Enhance allele bias calculation
#18
tfwillems
closed
6 years ago
0
Reduce visualization file size
#17
tfwillems
closed
7 years ago
0
Generalize STR calling to allow for multiple STR blocks
#16
tfwillems
closed
7 years ago
1
non-model organism, hipSTR is terminated at certain loci, doesnt accept multiple bam-samples in the list, doesn't find supplied chromosomes(scaffolds) as targets
#15
estolle
closed
8 years ago
6
Correctly visualize unspanned insertions in left tails
#14
tfwillems
opened
8 years ago
0
SIGFPE on downsampled data
#13
holtgrewe
closed
8 years ago
3
Obtaining TRF BED File
#12
holtgrewe
closed
8 years ago
2
Are there issues with many related samples?
#11
holtgrewe
closed
8 years ago
1
Left align flanking indels
#10
tfwillems
closed
8 years ago
2
Remove PCR duplicates
#9
tfwillems
closed
9 years ago
0
Indel tracking in flanking sequences
#8
tfwillems
closed
9 years ago
1
Flexible and correct response to --ref-vcf arguments
#7
tfwillems
closed
9 years ago
0
Alignment visualization issue
#6
tfwillems
closed
9 years ago
1
Optimize HMM deletion handling
#5
tfwillems
closed
9 years ago
0
Alignment traceback
#4
tfwillems
closed
9 years ago
1
Bgzip
#3
tfwillems
closed
9 years ago
0
Bootstrap option
#2
tfwillems
closed
9 years ago
1
Output gzipped VCFs
#1
tfwillems
closed
9 years ago
1
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