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50 results • Page
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Showing top results for tag:
gatk
•
reset
0
votes
3
replies
91
views
Mutect2 vcf.stats file missing
GATK
mutect2
vcf.stats
updated 11 hours ago by
Ram
32k • written 1 day ago by
rugarem
• 0
0
votes
2
replies
71
views
GATK no "SB" annotation after GenotypeGVCFs
gatk
strandbias
1 day ago by
wang.yiguan
• 0
1
vote
0
replies
51
views
Parallel haplotyping
gVCF
GATK
HaplotypeCaller
merge
parallel
2 days ago by
Poshi
▴ 10
0
votes
2
replies
80
views
GATK 4 and Spark multithreading
multithreading
haplotypecaller
sparks
gatk
15 hours ago by
Victoria
• 0
0
votes
0
replies
71
views
CNV-calling single sample
copynumbervariation
cnv
GATK
na12878
4 days ago by
Boberoni
• 0
3
votes
9
replies
1.0k
views
GATK Mutect2 Panel-Of-Normals generation
gatk
mutect2
panel-of-normal
wes
non-tumor
updated 3 days ago by
DIG
• 0 • written 9 months ago by
cocchi.e89
▴ 140
0
votes
0
replies
47
views
what are the parameters we should change when we run VariantsToTable of GATK in splitting multi allelic mode?
variantstotable
gatk
vcf
picard
6 days ago by
dare_devil
★ 1.4k
0
votes
0
replies
52
views
Active regions determination in HaplotypeCaller
SNP
GATK
VCF
HaplotypeCaller
BAM
8 days ago by
Nawar
• 0
2
votes
1
reply
98
views
Picard and GaTK HaplotypeCaller
gatk
picard
haplotypecaller
duplicates
updated 9 days ago by
prasundutta87
▴ 470 • written 10 days ago by
Afzal
• 0
0
votes
0
replies
86
views
How important is aligning BAM files to the appropriate design file?
gatk
sequencing
genomics
wes
bam
15 days ago by
jon.klonowski
▴ 70
1
vote
3
replies
193
views
HaplotypeCallerSpark
Variant
gatk
haplotypecaller
updated 15 days ago by
Pierre Lindenbaum
135k • written 15 days ago by
quentin54520
• 0
0
votes
2
replies
171
views
I use Mutects of Variant Call for paired Tumor/Normal WES, do I get a credibility (p value) for each call?
Mutect2
GATK
WES
Funcotator
9 days ago by
field654
▴ 10
3
votes
5
replies
2.5k
views
VariantsToTable in GATK does not produce the table of all SNPs in the vcf file
GATK
updated 21 days ago by
BunnyBosZ
• 0 • written 2.7 years ago by
Ana
▴ 180
1
vote
2
replies
603
views
htsjdk.tribble.TribbleException: The provided VCF file is malformed at approximately line number 92283: Duplicate allele added to VariantContext: C, …
VariantsToTable
vcf
gatk
17 days ago by
dare_devil
★ 1.4k
0
votes
1
reply
158
views
Trouble in SNP calling using GATK HaplotypeCaller
gatk
genome
updated 25 days ago by
devarora
▴ 430 • written 25 days ago by
pengxw1990
• 0
0
votes
0
replies
107
views
SAM: why NM and MD tag are changed by the picard tool SetNmMdandUqtag ?
alignment
gatk
sam
25 days ago by
quentin54520
• 0
0
votes
0
replies
129
views
germline vs somatic CNV GATK calling
CNV
germline
somatic
GATK
WGS
28 days ago by
cocchi.e89
▴ 140
1
vote
2
replies
94
views
merge paired-end sequencing
SNP
merge
gatk
28 days ago by
gubrins
▴ 70
0
votes
0
replies
88
views
Should i calculated Nm, UQ and MD tag of bam ?
alignment
bam
gatk
4 weeks ago by
quentin54520
• 0
0
votes
2
replies
103
views
Bam splitting index .sbi ?
alignment
index
gatk
updated 4 weeks ago by
Pierre Lindenbaum
135k • written 4 weeks ago by
quentin54520
• 0
0
votes
1
reply
134
views
[WGS] how to correctly visualize long indels (50nt+)
wgs
indel
visualization
igv
gatk
4 weeks ago by
memento1984_1
• 0
0
votes
0
replies
179
views
Variant Calling when Genetic Distance between Reference and Samples is Greater than it is for Humans: Does GATK still perform well?
GATK
variant calling
MASH
5 weeks ago by
robertwhbaldwin
• 0
1
vote
0
replies
107
views
Contig Ploidy Model
gatk
DetermineGermlineContigPloidy
5 weeks ago by
akshitiz09
▴ 10
1
vote
4
replies
101
views
Malformed BAM while running GATK
GATK
BAM
Read group
Barcode
5 weeks ago by
shivangi.agarwal800
▴ 70
5
votes
5
replies
211
views
How to convert gvcf file to normal vcf file ?
gatk
vcf
gvcf
updated 5 weeks ago by
devarora
▴ 430 • written 5 weeks ago by
dare_devil
★ 1.4k
0
votes
0
replies
106
views
Gatk spark beta
gatk
genome
spark
5 weeks ago by
quentin54520
• 0
0
votes
0
replies
99
views
Graphtyper vs GATK
Graphtyper
GATK
5 weeks ago by
Friyunnwoo
▴ 20
1
vote
5
replies
197
views
GATK VCF output: where are the sample-level annotations?
SNP
sequence
GATK
VCF
5 weeks ago by
mcrepeau
▴ 10
0
votes
0
replies
105
views
Calculating ROHs and Heterozygosity from GATK
ROHs
GATK
Heterozygosity
6 weeks ago by
gubrins
▴ 70
0
votes
2
replies
1.2k
views
use gatk phased vcf as input file of HapCut2
HapCut2
gatk
phasing
vcf
6 weeks ago by
Peter Chung
▴ 140
0
votes
0
replies
70
views
Multiple Sequencing Platforms, One Interval File?
WES
sequencing
GATK
6 weeks ago by
jon.klonowski
▴ 70
0
votes
5
replies
201
views
High CPU of GATK and Picard programs
GATK
java
cpu
RAM
updated 6 weeks ago by
Biostar
20 • written 3 months ago by
ognjen011
▴ 200
0
votes
2
replies
168
views
Variant calling tool for Bacterial NGS data
SNP
Variant calling
Bacterial
GATK
updated 6 weeks ago by
Biostar
20 • written 7 weeks ago by
Boberoni
• 0
1
vote
2
replies
245
views
Why GATK output haploid GT(genotype) even though my samples are diploid?
gatk
vcf
6 weeks ago by
haruki
▴ 10
0
votes
0
replies
92
views
How can I analyze a VCF dataset without an annotated reference genome
RNA-Seq
R
genome
gatk
galaxy
7 weeks ago by
julianneradford
• 0
0
votes
1
reply
93
views
Best (GATK compatible) RadSeq/GBS pipeline in 2021
radseq
gbs
gatk
7 weeks ago by
William
★ 4.8k
0
votes
1
reply
172
views
GATK tool to merge INDEL with SNPs with the same set of samples
VCF
GATK
updated 7 weeks ago by
Biostar
20 • written 11 weeks ago by
MAPK
★ 1.7k
0
votes
2
replies
358
views
Understanding GATK evaluation metrics
next-gen
snp
GATK
metrics
updated 7 weeks ago by
cdm4672
• 0 • written 7 months ago by
geneart$$
▴ 40
1
vote
11
replies
205
views
GATK HaplotypeCaller Error
software error
rna-seq
gatk
8 weeks ago by
sahar.salimi92
• 0
0
votes
1
reply
141
views
Experience with BaseRecalibratorSpark and ApplyBQSRSpark
gatk
somatic
mutations
snp
updated 8 weeks ago by
colindaven
★ 2.7k • written 8 weeks ago by
nickhir
▴ 30
0
votes
3
replies
201
views
which tool should be used to call the genotype?
ngs
genotype
gatk
genotype calling
variant
updated 8 weeks ago by
Biostar
20 • written 3 months ago by
JENNIE
• 0
1
vote
4
replies
217
views
Checking ReadGroup name in BAM file error: E26: Hebrew cannot be used: Not enabled at compile time
RNA-Seq
GATK
updated 8 weeks ago by
Pierre Lindenbaum
135k • written 8 weeks ago by
julianneradford
• 0
1
vote
1
reply
123
views
Are there any repository for panel of normal for running Mutect2?
Mutect2
PON
panel of normal
gatk
8 weeks ago by
dare_devil
★ 1.4k
0
votes
0
replies
144
views
Panel of normals for Mutect2 GRCh37
gatk
broad
mutect2
8 weeks ago by
nickhir
▴ 30
0
votes
2
replies
158
views
Calling variants on reads with MAPQ=0 on HaplotypeCaller or bcftools mpileup
whole-exome-sequencing
variants
GATK
hg19
updated 8 weeks ago by
Pierre Lindenbaum
135k • written 8 weeks ago by
Anupriya Dalmia
• 0
1
vote
2
replies
121
views
No overlapping contigs found.
ChIP-Seq
GATK
8 weeks ago by
L_LANKA
• 0
1
vote
3
replies
161
views
NGS/GATK pipeline returns too many variants
NGS
WES
GATK
Mutect
9 weeks ago by
dodausp
▴ 150
1
vote
2
replies
138
views
Extract below 100% overlapping intervals among samples from WGS data
WGS
bedtools
GATK
updated 9 weeks ago by
Pierre Lindenbaum
135k • written 9 weeks ago by
FL512
• 0
1
vote
1
reply
186
views
GATK HaplotypeCaller Error
RNA-Seq
GATK
HaplotypeCaller
Java
Error
updated 9 weeks ago by
Pierre Lindenbaum
135k • written 9 weeks ago by
julianneradford
• 0
0
votes
0
replies
130
views
Refseq file 0 coding length
gatk
DepthOfCoverage
updated 10 weeks ago by
lieven.sterck
10k • written 10 weeks ago by
whb
▴ 20
50 results • Page
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