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<prev • 476 results • page 1 of 16 • next >
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GATK error message: Badly formed genome location
gatk genotype calling written 3 days ago by jtwalker • 10
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1
answer
167
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1
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Why people use gatk v2.3.9lite?
gatk written 5 days ago by bluemonster0808 • 0 • updated 5 days ago by h.mon ♦ 8.0k
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149
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1
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Merging BAM file before running GATK or merging vcf output
vcf gatk snp written 8 days ago by pbigbig • 180 • updated 8 days ago by Lila M • 320
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1
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204
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rna seq genome coverage
gatk picard coverage rna-seq written 10 days ago by ea1402 • 10 • updated 10 days ago by geek_y ♦ 7.8k
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Filtering on MAF using the GATK?
variant filtering gatk snp filtering written 4 weeks ago by jtwalker • 10 • updated 17 days ago by Biostar ♦♦ 20
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1
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126
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Is GATK overestimating the heterozygous calls?
vcf gatk heterozygous snp written 23 days ago by biobudhan • 10 • updated 23 days ago by andrew.j.skelton73 • 3.6k
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115
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Combine VCF files with multiple alternative alleles in GATK
gatk ngs sequencing combine variants calling written 26 days ago by ciemanek • 20
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1
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137
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1
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Making a vcf file from a subset of regions from gvcf files
vcf gatk written 29 days ago by Floris Brenk • 790 • updated 26 days ago by aays • 60
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1
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160
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1
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GATK VariantFiltration invalid expression
filtration gatk ngs variants written 28 days ago by ciemanek • 20 • updated 28 days ago by finswimmer • 360
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1
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157
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1
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GATK variantFiltration unexpected behaviour?
gatk variant filtration snp written 4 weeks ago by jtwalker • 10
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1
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248
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GATK: SAM file doesn't have any read groups defined in the header.
gatk rna-seq written 4 weeks ago by mahnoornaseer97 • 0
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2
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189
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how to calling variants in RNAseq data from multiple samples?
variant calling gatk vc rna-seq written 5 weeks ago by Lila M • 320 • updated 4 weeks ago by Samuel Brady • 230
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164
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variant calling discondordance between same sample between two run
disconcordance gatk abratio written 5 weeks ago by J.F.Jiang • 640
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2
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166
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Feasible Annotation of 4 million unique SNPs
gatk ase snp written 5 weeks ago by serpalma.v • 10 • updated 5 weeks ago by Emily_Ensembl ♦ 12k
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123
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dbsnp file for C. elegans
gatk dbsnp c. elegans variation file written 5 weeks ago by cristian • 70
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1
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310
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How to filter mutect2 VCF output?
gatk alignment snp mutect2 written 7 weeks ago by Whoknows • 580 • updated 5 weeks ago by poisonAlien • 2.4k
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1
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165
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1
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GATK: SNP coverage too high?
gatk written 6 weeks ago by Marvin • 90 • updated 6 weeks ago by harold.smith.tarheel • 3.7k
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1
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352
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1
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HapCUT2 using GATK results
hapcut2 gatk vcf phasing written 6 months ago by jyu429 • 120 • updated 6 weeks ago by lloydlow • 0
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143
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simulating variants with specific frequency using GATK
vcf gatk written 8 weeks ago by christacaggiano • 20 • updated 6 weeks ago by Biostar ♦♦ 20
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1
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195
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1
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snpEff database to annotate b37 GATK output
gatk snpeff written 4 months ago by Helene • 390 • updated 8 weeks ago by hns • 130
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1
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177
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1
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How to only show SNPs in vcf files
vcf gatk snp written 9 weeks ago by Joe • 30 • updated 9 weeks ago by Pierre Lindenbaum ♦ 96k
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145
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VCFtools intersect vs. GATK intersect
vctfools gatk intersect snp sequencing written 9 weeks ago by ciemanek • 20 • updated 9 weeks ago by Pierre Lindenbaum ♦ 96k
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181
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How to set the GATK_PATH of PolySolver
gatk hla polysolver samtofastq written 10 weeks ago by shiyang93 • 10
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1
answer
129
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1
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Pindel and GATK AD Concordance
variant calling gatk allele depth pindel written 10 weeks ago by jsneaththompson • 0 • updated 10 weeks ago by Dan Gaston ♦ 6.8k
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158
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VQSLOD score different for Full and split (by chromosome) BAM file
vcf gatk written 4 months ago by dasdevashishdas • 120 • updated 11 weeks ago by Biostar ♦♦ 20
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3
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507
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7 follow
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Getting error in running GATK (GenomeAnalysisTK-3.7)?
gatk picard mutation rna-seq written 5 months ago by Mask • 220 • updated 11 weeks ago by LLinging00 • 0
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News: GATK returns to a fully open-source license
gatk news written 12 weeks ago by Istvan Albert ♦♦ 73k
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7 follow
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What Are The Open Source Alternatives To Gatk?
gatk written 4.5 years ago by scottsmith1 • 180 • updated 12 weeks ago by Brian Bushnell ♦ 13k
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4
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Open Source Compliant Diploid Variant Caller comparable to GATK Haplotype Caller?
variant calling gatk written 2.9 years ago by 14134125465346445 • 3.3k • updated 12 weeks ago by vdauwera • 560
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298
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6 follow
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GATK - gene panel VCF - too many variants - how to filter out
vcf gatk ngs written 3 months ago by stanedav • 10
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