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CSB5
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lofreq
LoFreq Star: Sensitive variant calling from sequencing data
http://csb5.github.io/lofreq/
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Handling of soft-clipped bases
#94
rspreafico-vir
closed
4 years ago
2
No output?
#93
vymao
opened
4 years ago
3
Error when specifying --min-cov parameter
#92
cjuigne
closed
4 years ago
2
LOFreq Improvements for HPC - buffers
#91
lflis
opened
4 years ago
7
LoFreq 2.1.4 indelqual -dindel issue writing to stdout
#90
smrey
opened
4 years ago
7
LoFreq 2.4 indelqual filter error
#89
sleyn
closed
4 years ago
65
BD/BI tags are missing (no indels were called)
#88
sleyn
closed
4 years ago
1
Official tag for 2.1.4?
#87
johnnygenomics
closed
4 years ago
1
Convert lofreq to use the HTSlib API instead of the legacy samtools API
#86
jmarshall
closed
4 years ago
2
call_pparallel without filtering produces vcf.gz unconditionally
#85
wm75
closed
4 years ago
4
effect of capping MQ on reads with MQ 255
#84
wm75
closed
4 years ago
3
Option to force calls at specific sites?
#83
JesseDGibson
closed
4 years ago
1
LofreqSomatic not calling indel which was called by Lofreq and other callers
#82
stevekm
closed
4 years ago
2
DP and DP4 do not add up for indels
#81
ivan-mh
opened
5 years ago
0
How are AFs computed?
#80
romagnolid
opened
5 years ago
9
put in check for counts of commands/contigs
#79
brandonlind
opened
5 years ago
0
Insertions around homopolymers
#78
jonaudet
opened
5 years ago
0
Strand Bias in unidirectional reads
#77
abolia
closed
5 years ago
2
Strand bias incorrectly computed in areas with unidirectional reads
#76
brendanofallon
closed
5 years ago
1
lofreq2_add_fake_gt.py python 3 support
#75
igordot
opened
5 years ago
3
Duplicated variants reported
#74
romagnolid
closed
5 years ago
7
Can I use the value of QD (QUAL/DP) to filter the result of Lofreq?
#73
Tiredbird
closed
4 years ago
2
Indels not written to the VCF file
#72
abolia
closed
4 years ago
3
Lofreq vcfplot error
#71
jatintalwar
opened
5 years ago
1
include tools scripts in bioconda build
#70
Smeds
opened
5 years ago
6
FATAL(plp.c|compile_plp_col:947): Base qualitiy above allowed maximum detected (255)
#69
jnarayan81
closed
5 years ago
1
minimum bq error not reported correctly in call-parallel`
#68
map2085
opened
6 years ago
0
what is the default filter?
#67
map2085
closed
5 years ago
3
Can it call variants on tetraploid species?
#66
afzm
closed
6 years ago
3
Threads command raise error
#65
looxon93
opened
6 years ago
0
Compilation problem
#64
looxon93
closed
6 years ago
7
Downsample option
#63
andreas-wilm
opened
6 years ago
0
Speedup possible by applying early minimum AF filter
#62
andreas-wilm
opened
6 years ago
0
lofreq installation error ?
#61
pinninti19
closed
6 years ago
1
it is suitable for somatic calling without normal ?
#60
WinterLi1993
closed
6 years ago
4
"lofreq_call.c|call_snvs" Skipped when running on bam containing N cigar operator (RNA-seq)
#59
akkellogg
opened
6 years ago
4
germline calls for lofreq somatic
#58
sraorao
closed
6 years ago
2
VCF file format
#57
WashingtondaSilva
closed
4 years ago
2
lofreq call with --no-default-filter
#56
thakki
opened
6 years ago
2
lofreq call filter doesn't work
#55
Lien-NGSdummie
closed
6 years ago
3
Could not parse threshold
#54
zipho
closed
7 years ago
4
VCF sample column
#53
igordot
closed
7 years ago
7
Issue when run make
#52
WashingtondaSilva
closed
4 years ago
7
Unable to run call-parallel on filenames with spaces
#51
ozagordi
opened
7 years ago
4
lofreq working on both python 2 and 3
#50
ozagordi
closed
7 years ago
4
DP and DP4 fields
#49
abolia
closed
7 years ago
3
SyntaxError: Non-ASCII character '\xb6' in file lofreq_star-2.1.2/
#48
wdemos
closed
7 years ago
4
Substitution and indel tests
#47
zeus19900814
closed
7 years ago
12
Quality scores capped at 49314
#46
abolia
opened
7 years ago
2
The variants of Low frequence
#45
Tinalxt
closed
7 years ago
3
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