Latest
Open
RNA-Seq
ChIP-Seq
SNP
Assembly
Tutorials
Tools
Jobs
Forum
Planet
All »
Home
Log In
Showing: gatk • reset
or   Classic search
<prev • 662 results • page 1 of 23 • next >
1
vote
1
answer
48
views
1
answer
Why do we need a .fai file and a .dict file of the reference during alignment and variant calling using GATK?
sequencing gatk next-gen file_formats alignment written 4 hours ago by Cookie-san • 0 • updated 2 hours ago by Pierre Lindenbaum ♦ 119k
6
votes
0
answers
144
views
0
answers
GATK HaplotypeCaller Problems
software error gatk next-gen alignment written 4 weeks ago by chengye • 10 • updated 20 hours ago by Biostar ♦♦ 20
1
vote
0
answers
74
views
0
answers
Mutect2 "somatic" variants with resistant tissue culture lines
gatk wes mutect2 variants genotyping written 11 days ago by shawn.w.foley • 400 • updated 3 days ago by Biostar ♦♦ 20
0
votes
0
answers
118
views
0
answers
How to run R docker in WDL?
wdl R cromwell docker gatk written 5 days ago by c.clarido • 40
0
votes
0
answers
58
views
0
answers
How fix error "INVALID_MATE_REF_INDEX" in a SAM/BAM file of NGS data?
gatk next-gen sam/bam file written 9 days ago by zamani_2012 • 0
0
votes
2
answers
96
views
2
answers
Genotype file supporting gatk CalculateGenotypePosteriors
wgs gatk genotyping written 5 weeks ago by gwotto • 0
0
votes
1
answer
100
views
1
answer
GATK best practice step-by-step command lines for Arabidopsis DNA-Seq data analysis
gatk dna-seq arabidopsis written 13 days ago by wangdp123 • 140 • updated 13 days ago by Pierre Lindenbaum ♦ 119k
0
votes
0
answers
137
views
0
answers
GATK genomicsDBimport intervals for WGS
gatk genomicsdbimport written 16 days ago by Nicolas Rosewick ♦ 7.5k
8
votes
2
answers
2.5k
views
11 follow
2
answers
Is there a easy to use GATK pipeline for SNP calling?
gatk written 12 months ago by Chen • 830 • updated 14 days ago by johannes.koester • 10
7
votes
1
answer
248
views
1
answer
GATK failing to find any variants - how to troubleshoot?
gatk rna-seq written 26 days ago by Kristin Muench • 410
0
votes
0
answers
90
views
0
answers
Gatk Mutec2 germline resources for mouse
gatk sequencing mm10 written 19 days ago by tarekzakaria.badr • 30 • updated 19 days ago by h.mon ♦ 24k
1
vote
1
answer
117
views
1
answer
Extracting information from gatk VariantFiltration output
gatk wgs written 20 days ago by F • 3.4k
7
votes
1
answer
123
views
7 follow
1
answer
Can you use germline variation calling on a normal embryonic stem cell line?
germline variation gatk wes snp embryonic cell written 21 days ago by maria2019 • 10 • updated 21 days ago by Emily_Ensembl ♦ 18k
0
votes
0
answers
68
views
0
answers
Difference between HC and UG methods
gatk next-gen algorithm sequencing written 21 days ago by chengye • 10
5
votes
3
answers
1.5k
views
8 follow
3
answers
GATK - gene panel VCF - too many variants - how to filter out
vcf gatk ngs written 23 months ago by stanedav • 30 • updated 21 days ago by Biostar ♦♦ 20
0
votes
0
answers
89
views
0
answers
What is the tlod in vcf?
gatk tlod mutect2 written 23 days ago by 2yuna710 • 0
1
vote
1
answer
100
views
1
answer
snp identification with Haplotypecaller and SelectVariants
gatk snp written 29 days ago by felipead66 • 30 • updated 29 days ago by Pierre Lindenbaum ♦ 119k
2
votes
1
answer
111
views
6 follow
1
answer
VariantFiltration warning "undefined variable"
gatk variantfiltration error written 4 weeks ago by felipead66 • 30 • updated 4 weeks ago by Pierre Lindenbaum ♦ 119k
0
votes
1
answer
94
views
1
answer
GATK PrintRead Producing Empty File
gatk printread written 4 weeks ago by BAGeno • 120 • updated 4 weeks ago by Pierre Lindenbaum ♦ 119k
1
vote
1
answer
111
views
1
answer
ASEReadCounter More then one variant context at position
selectvariants gatk asereadcounter written 5 weeks ago by mb2subi • 0 • updated 4 weeks ago by Charles Warden ♦ 6.5k
0
votes
1
answer
131
views
1
answer
Merging variant calls of whole exome and RNA-seq
snvs gatk variants rna-seq indels written 5 weeks ago by Saad Khan • 330 • updated 5 weeks ago by archie • 70
0
votes
0
answers
145
views
0
answers
Remove symbolic alleles for REF in a VCF file.
vcf gatk ngs gvf baserecalibrator written 5 weeks ago by pmorellmi • 0
0
votes
2
answers
207
views
2
answers
Removing or not removing the duplicates in .bam file
gatk picard rna-seq wgs written 6 weeks ago by F • 3.4k
0
votes
0
answers
78
views
0
answers
how to run GATK CalculateGenotypePosteriors on a case-control cohort
gatk calculategenotypeposteriors written 6 weeks ago by blueskypie • 30
0
votes
1
answer
168
views
1
answer
How treat a Bam file with mutiple read groups (RG)
gatk next-gen picard read group bam written 6 weeks ago by zamani_2012 • 0 • updated 6 weeks ago by Pierre Lindenbaum ♦ 119k
0
votes
0
answers
80
views
0
answers
Mutect v1 doesnt finds second alternative allele
gatk next-gen mutect somatic written 6 weeks ago by guffrann • 0
1
vote
3
answers
2.3k
views
3
answers
Where To Get The Annotation File For The Nimblegen Seqcap Ez Exome V1
exome gatk variant bwa written 5.9 years ago by ewre • 220 • updated 6 weeks ago by 477926757 • 0
1
vote
0
answers
206
views
0
answers
SNP Calling Parameter Settings
vcf gatk snp written 12 weeks ago by mcclintock • 10 • updated 6 weeks ago by Biostar ♦♦ 20
2
votes
1
answer
248
views
1
answer
VCFParseError: ploidy > 2 not supported
vcf gatk ploidy written 3 months ago by always_learning • 960 • updated 6 weeks ago by tpoterba • 40
3
votes
2
answers
156
views
2
answers
Variant calling in large sample populations
genome gatk sequence sequencing written 7 weeks ago by robjohn70000 • 120 • updated 7 weeks ago by Pierre Lindenbaum ♦ 119k
<prev • 662 results • page 1 of 23 • next >
Recent Votes
Recent Locations • All »
  • United States, 1 minute ago
  • Sweden, 2 minutes ago
  • Boston, 2 minutes ago
  • United Kingdom, 2 minutes ago
  • France/Nantes/Institut du Thorax - INSERM UMR1087, 8 minutes ago
Recent Awards • All »
Recent Replies
Content
Help
Access
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1492 users visited in the last hour