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lindenb
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jvarkit
Java utilities for Bioinformatics
https://jvarkit.readthedocs.io/
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SamViewWithMate: width one regions using BED file
#154
daynefiler
closed
4 years ago
2
[FixVcfMissingGenotypes]partial missing values for GL field, Ignoring SAM validation error, and [Launcher]fixvcfmissinggenotypes Exited with failure (-1)
#153
jdalapicolla
closed
4 years ago
4
Add -a,--all option to cmpbams so it compares all reads
#152
lckarssen
closed
4 years ago
2
Missing read from cmpbams output?
#151
lckarssen
closed
4 years ago
4
Does cmpbams support CRAMs?
#150
lckarssen
closed
4 years ago
3
[SEVERE][CoverageServer]Cannot figure out type of file file:///home/silviav/jvarkit/fasta from extension
#149
Caro-Ca
opened
4 years ago
12
error when compiling biostar251649
#148
kevin-oh
closed
4 years ago
5
Is there a specifier that could be used in the BlastToSnp command line that would not eliminate perfect matches that are in the output blastn file?
#146
deborapirespaula
closed
4 years ago
1
Biostar404363 build failing, gradle cannot download htsjdk
#145
690645258
closed
4 years ago
2
[INFO][Launcher]bim2vcf Exited with failure (-1)
#144
vicruiser
opened
4 years ago
8
insertions not shown in sam2tsv results ja
#143
Huanle
closed
4 years ago
15
vcf2table output files problem
#142
motutaj
closed
4 years ago
6
ERROR IN VCF HEADER
#141
AqsaMajeed-star
opened
4 years ago
1
Error in partial missing values for GL field
#140
arouette
closed
4 years ago
3
Minor changes to bamwithoutbai paper
#139
tomwhite
closed
4 years ago
0
install error ?
#138
hmyh1202
opened
4 years ago
3
Vcfrebase requires "ENZ" to be defined in VCF header and unsure of ENZ field format
#137
jelber2
closed
4 years ago
6
no reads output with bamslicebed
#136
vibansal
closed
4 years ago
3
Can I use biostar160470.jar with a psi-tBLASTn checkpint file as query?
#135
cosmiccapybara
opened
5 years ago
2
biostar160470 Exited with failure (-1) parser error : Premature end of data in tag Iteration_hits line 1105
#134
cosmiccapybara
closed
5 years ago
7
sam2tsv: Errormessage: Index 0 out of bounds for length 0
#133
joachimwolff
closed
5 years ago
5
vcf2mongo.xslt missing
#132
darked89
closed
5 years ago
2
deletion without obvious coverage drop in the depth panel
#131
shannjiang
opened
5 years ago
0
Extraction fails for entire chromosome
#130
sum732
closed
5 years ago
6
Running gradlew on sortsamrefname returns zip END header not found errors
#129
martinbaste
closed
5 years ago
1
sortsamrefname fails with "java.nio.file.FileSystemException: ... Too many open files"
#128
Martingales
closed
4 years ago
2
New release for bioconda?
#127
guillaumecharbonnier
closed
5 years ago
2
deletion shown by lowresbam2raster
#126
shannjiang
closed
5 years ago
2
Problem : CHROM header line
#125
vicbp1
closed
5 years ago
6
samjdk information
#124
orspa
opened
5 years ago
5
[INFO][Launcher]bamstats04 Exited with failure (-1): bam is not indexed
#123
innagsc
closed
4 years ago
9
An exception in running sam2tsv.jar
#122
weir12
closed
5 years ago
12
samextractclip not working on Minimap2 SAM file
#121
MaestSi
closed
5 years ago
6
javax.annotation does not exist
#120
DavideGue
closed
5 years ago
3
reference
#119
jinyoungkoh
opened
5 years ago
2
advice about a program similar to blast2snp for tblastn results
#118
rbatorsky
closed
5 years ago
2
biostar103303 error: no exon found
#117
giuseppedelnapalle
closed
5 years ago
9
class not found
#116
bgphd
opened
5 years ago
8
I have had success installing jvarkit on Mac in the past, but now problems on CentOS
#115
bgphd
closed
5 years ago
2
SAM2TSV OUTPUT: reference position is not always 0-based?
#114
Huanle
closed
5 years ago
4
bamstats05 ERROR : error msg : Exited with failure (-1)
#113
Vithyanatarajan
closed
5 years ago
3
bamstats04
#112
patidarr
closed
5 years ago
1
does Sam2Tsv only print out variants but no perfect matches?
#111
Huanle
closed
6 years ago
2
fix gap filling string in fastq file
#110
y9c
closed
6 years ago
10
Can sam4weblogo output the read quality in the aligned fastq file, instead of a fasta file.
#109
y9c
closed
6 years ago
3
biostar214299 handles some of the soft clipped reads incorrectly
#108
Glombas
closed
6 years ago
2
Processing the output .vcf file from msa2vcf
#107
MostafaYA
closed
6 years ago
1
Errors installing Bam2Raster tool
#106
xiucz
closed
6 years ago
1
msa2vcf
#105
vinay104
closed
6 years ago
1
Extract PE Reads (with their mates) supporting variants in vcf file (www.biostars.org/p/322664/)
#104
Pitithat-pu
closed
6 years ago
9
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