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<prev • 459 results • page 1 of 16 • next >
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simulating variants with specific frequency using GATK
vcf gatk written 3 days ago by christacaggiano • 20
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1
answer
138
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1
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snpEff database to annotate b37 GATK output
gatk snpeff written 9 weeks ago by Helene • 370 • updated 6 days ago by hns • 130
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1
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102
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1
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How to only show SNPs in vcf files
vcf gatk snp written 8 days ago by Joe • 20 • updated 8 days ago by Pierre Lindenbaum ♦ 95k
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86
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VCFtools intersect vs. GATK intersect
vctfools gatk intersect snp sequencing written 12 days ago by aagata.szymanek • 10 • updated 12 days ago by Pierre Lindenbaum ♦ 95k
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91
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How to set the GATK_PATH of PolySolver
gatk hla polysolver samtofastq written 15 days ago by shiyang93 • 10
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1
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Pindel and GATK AD Concordance
variant calling gatk allele depth pindel written 16 days ago by jsneaththompson • 0 • updated 16 days ago by Dan Gaston ♦ 6.8k
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117
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VQSLOD score different for Full and split (by chromosome) BAM file
vcf gatk written 11 weeks ago by dasdevashishdas • 120 • updated 23 days ago by Biostar ♦♦ 20
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3
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319
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5 follow
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Getting error in running GATK (GenomeAnalysisTK-3.7)?
gatk picard mutation rna-seq written 3 months ago by Snijesh • 0 • updated 25 days ago by LLinging00 • 0
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News: GATK returns to a fully open-source license
gatk news written 4 weeks ago by Istvan Albert ♦♦ 71k
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7 follow
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What Are The Open Source Alternatives To Gatk?
gatk written 4.4 years ago by scottsmith1 • 180 • updated 4 weeks ago by Brian Bushnell ♦ 12k
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4
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4
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Open Source Compliant Diploid Variant Caller comparable to GATK Haplotype Caller?
variant calling gatk written 2.7 years ago by 14134125465346445 • 3.2k • updated 4 weeks ago by vdauwera • 550
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3
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203
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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 6 weeks ago by stanedav • 10
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RealignerTargetCreator inputs multiple Bams??
gatk bam realignertargetcreator written 5 weeks ago by micro32uvas • 0 • updated 5 weeks ago by Devon Ryan ♦ 68k
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How to build reference for an artificial reporter sequence in GATK?
gatk amplicon reference written 5 weeks ago by yinboz • 0
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2
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178
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2
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News: Webinar on fast and accurate DNA variant calling on 26 Apr 2017
variant calling news snp gatk alignment strand ngs written 9 weeks ago by strandbiz • 40
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140
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pre-processing whole genome data
dbsnp.vcf gatk rhesus macaque written 7 weeks ago by br.tania • 0 • updated 7 weeks ago by genomax ♦ 29k
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150
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Understanding VCF file for downstream analysis
vcf gatk snp written 8 weeks ago by upendrakumar.devisetty • 340
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1
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141
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1
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What is ploidy level for HaplotypeCaller ?
genome gatk snp written 8 weeks ago by mirzaei86.vahid • 10 • updated 8 weeks ago by WouterDeCoster ♦ 19k
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1
answer
142
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1
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Malformed BAM file produced by BWA
gatk picard samtools written 8 weeks ago by joreamayarom • 80 • updated 8 weeks ago by Pierre Lindenbaum ♦ 95k
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1
answer
139
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1
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Do I have to realign from scratch?
gatk incompatible contigs written 8 weeks ago by Kasthuri • 210 • updated 8 weeks ago by genomax ♦ 29k
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185
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Any comparisons of read length for variant calling?
assembly next-gen variant snp gatk written 8 weeks ago by Sukhdeep Singh ♦ 8.8k • updated 8 weeks ago by Brian Bushnell ♦ 12k
21
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5
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13k
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15 follow
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How To Split Multiple Samples In Vcf File Generated By Gatk?
vcf gatk split written 3.9 years ago by newDNASeqer • 550 • updated 9 weeks ago by Biostar ♦♦ 20
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1
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141
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1
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Variant callers reporting different read depth on same alignment
variant calling gatk freebayes variant annotation written 9 weeks ago by murrayln • 10 • updated 9 weeks ago by Pierre Lindenbaum ♦ 95k
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1
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223
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GATK haplotypecaller can be restricted to specific intervals using -L option, but can we add other information with interval files to the VCF?
haplotypecaller gatk snp interval list genotyping written 10 weeks ago by Hemant Gupta • 0 • updated 10 weeks ago by Pierre Lindenbaum ♦ 95k
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205
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5 follow
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News: Workshop: GATK Best Practices for Variant Discovery, Edinburgh, 17-19 July 2017
variant calling gatk news workshop written 10 weeks ago by Bert Overduin • 3.5k
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2
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5 follow
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COSMIC vcf file compatibility for Mutect2
vcf gatk mutect2 cosmic written 5 months ago by erwan.scaon • 150
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1
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130
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1
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Outputting DP4 flag in GATK
variant calling gatk sequencing written 11 weeks ago by Jautis • 240 • updated 11 weeks ago by Santosh Anand • 2.3k
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170
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1
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GATK IndelGenotyperV2 error
gatk written 3 months ago by divya.srivastava33 • 10 • updated 11 weeks ago by Ray Lee • 0
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119
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Ts/Tv ratio of 1.7
exome gatk snpeff written 11 weeks ago by jarod_v6 • 10
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162
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Problems with read group in GATK
gatk read group sequencing written 12 weeks ago by kristincilla_16 • 0
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