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dkoboldt
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varscan
Variant calling and somatic mutation/CNV detection for next-generation sequencing data
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how to filter using vcf from multiple samples generated by mpileup2somatic
#67
weiydcn
opened
7 months ago
0
varscan2 output can't be fed to snpEff. ID column missing?
#66
gabrielet
opened
8 months ago
0
Why genotype and depth representations are inconsistent
#65
fjptwenger
opened
1 year ago
0
filter for pielup2cns not working
#64
zoeward-nz
opened
1 year ago
0
two mutations on one pos can't call out
#63
user-tq
opened
2 years ago
0
log4j
#62
myourshaw
opened
2 years ago
0
Reads supporting a variant
#61
biounix
opened
3 years ago
0
error download jar, corrupt or incomplete
#60
cmccabe0728
closed
3 years ago
1
How to pipe deovo trio with samtool mpileup?
#59
snijesh
opened
3 years ago
1
how to pipe the denovo trio calling?
#58
snijesh
closed
3 years ago
0
Not filtering reverse strand's strand bias
#57
svarona
opened
3 years ago
0
mpileup2snp do not detect all snps
#56
wwang-chcn
opened
4 years ago
0
NumberFormatException in varscan somatic
#55
Jasondai9
opened
4 years ago
1
Malformed VCF output
#54
jfnavarro
opened
4 years ago
0
Strand filter applied when outputting to tabular format but not VCF
#53
nh13
opened
4 years ago
0
2.4.4 "release" is actually source
#52
flowers9
opened
4 years ago
1
filtering error - "Too many parsing exceptions encountered"
#51
yeroslaviz
opened
4 years ago
1
0 had sufficient coverage for comparison
#50
jingmeng-bioinformatics
opened
4 years ago
1
Varscan mpileup2cns error: `Input file(s) were not ready for parsing after 100 5-second cycles`.
#49
besnarda
opened
4 years ago
0
Missing filters in VarScan fpfilter output VCF header
#48
Stikus
opened
5 years ago
1
Commas in the vcf-files_FILTER field
#47
golubnikova
opened
5 years ago
0
varscan report wrong DP related values, almost 50% off
#46
yingchen69
opened
5 years ago
2
pileup2snp output
#45
Eugene79
opened
5 years ago
0
Mergesegments.pl output question
#44
JuanmaMedina
opened
5 years ago
0
Ambiguous allele (UIPAC) not properly handled according to VCF specs 4.3
#43
huguesfontenelle
opened
5 years ago
2
MNV or two SNV
#42
aledj2
opened
5 years ago
1
Varscan trio de novo mutation calling too slow
#41
shannjiang
opened
5 years ago
0
False Positive SNP Calls
#40
eckofoid
opened
5 years ago
0
Suggestions for using Varscan2 on tumor only samples ?
#39
kmavrommatis
opened
5 years ago
1
somaticfilter default --min-reads2 value error
#38
GeorgetteTanner
opened
5 years ago
0
how to create the site list files for bam-read-count for the indels called by varscan2
#37
dingying85
opened
5 years ago
2
Can it call variants on tetraploid species?
#36
afzm
opened
6 years ago
0
varscan appears to throw out reverse reads
#35
graft
opened
6 years ago
0
varscan somatic terminates without error, sometimes with an error
#34
IanCodes
opened
6 years ago
1
Please use Git repository properly
#33
tillea
opened
6 years ago
0
varscan copynumber running problem
#32
jinxinhao0627
opened
6 years ago
1
typos returning fpfilter counts
#31
splaisan
opened
6 years ago
0
Redundant Processing To Get SNPs and Indels
#30
DarioS
opened
6 years ago
0
Enable Multiple CPUs To Be Used
#29
DarioS
opened
6 years ago
0
State Location of Output
#28
DarioS
opened
6 years ago
0
typos in doc
#27
splaisan
opened
6 years ago
1
Java version required is not listed
#26
lachlansimpson
opened
6 years ago
0
sanity error when running bcftools stats on varscan data
#25
splaisan
opened
6 years ago
0
min-mmqs-diff does not accept negative values.
#24
santanasantosl
opened
7 years ago
0
the num of +-strand diff greatly(Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev)
#23
liufengxia99
closed
7 years ago
2
VCF output for varscan somatic not working
#22
kmavrommatis
opened
7 years ago
5
Erroneous flags are passing silently.
#21
mikeraiko
opened
7 years ago
0
MinMMQSdiff
#20
iranmdl
opened
7 years ago
0
Infering population parameters from pooled samples
#19
situssog
opened
7 years ago
2
indel immediately following SNV is not called
#18
nstickle
opened
7 years ago
0
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