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<prev • 751 results • page 1 of 26 • next >
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Population / Reference bias in GATK BQSR BaseRecalibrator?
population bias gatk bqsr non model organism written 1 day ago by Andrés Ribone • 0
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1
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364
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6 follow
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Pipe SamToFastq, BWA mem not working
gatk sam bwa pipe written 4 months ago by abbysue • 10 • updated 1 day ago by Marco Pessoa • 0
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182
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stats file in Mutect2 calling
gatk written 10 weeks ago by dentepre • 0 • updated 4 days ago by vipulbhatia24 • 0
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Creating a panel of normal from one normal sample
variant-calling gatk mutect2 panelofnormals written 5 days ago by Jordan • 1.1k
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2
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86
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Undefined variable error in linux
sequencing seq linux gatk written 6 days ago by karthick.n • 10 • updated 6 days ago by Pierre Lindenbaum ♦ 124k
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soft-clipping during alignment and variant calling query
variant calling bwa-mem alignment gatk written 4 weeks ago by prasundutta87 • 360 • updated 11 days ago by Biostar ♦♦ 20
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How to treat heterozygous GATK calls on haploid chromosomes (sex chrom in males)
gatk snps haploid haplotype caller written 21 months ago by QVINTVS_FABIVS_MAXIMVS • 2.3k • updated 12 days ago by monicapenon • 0
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98
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How to get INFO tag "OREF" in vcf files
vcf gatk snp written 14 days ago by raulee • 0
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2
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227
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GATK Terra Best Practices pipeline for Mito Variant Calling
terra gatk wes variant calling written 8 weeks ago by a.j.wilson0000 • 10 • updated 15 days ago by houkto • 70
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CollectHsMetrics per_base_coverage results quirk
gatk mitochondrial variant calling written 27 days ago by a.j.wilson0000 • 10 • updated 19 days ago by houkto • 70
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82
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Fastq to VCF pipeline configuration for low coverage data
gatk deepvariant written 22 days ago by igor • 0
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61
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Recalibrated bam file is too small (~48K), fails on haplotypecaller
gatk applybqsr short variant detection written 23 days ago by Cricket • 10
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140
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1
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Filtering for individual allelic balance in multisample vcf using GATK4
vcf gatk gatk4 filtering written 27 days ago by mernster • 0 • updated 26 days ago by chrchang523 ♦ 5.8k
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How to get chrM chr1 ...chr22 chrX chrY order in my bam file
gatk picard snp bam sort written 27 days ago by Ada • 0 • updated 26 days ago by jkbonfield • 200
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1
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89
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1
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Using GATK AddOrReplaceReadGroups
gatk written 27 days ago by vctrm67 • 10 • updated 26 days ago by Pierre Lindenbaum ♦ 124k
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2
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282
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2
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GATK Error Message: Invalid argument value 'RealignerTargetCreator at position' 0
vcf gatk snp written 5 months ago by hafiz.talhamalik • 210 • updated 27 days ago by Mohammed • 10
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Generating a PoN with GATK CombineVariants using wildcards
vcf gatk written 29 days ago by graeme.thorn • 40
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1
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957
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1
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RealignerTargetCreator (GATK) contig issue
gatk written 22 months ago by win • 810 • updated 28 days ago by Biostar ♦♦ 20
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80
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Use of GATK HaplotypeCallerSpark
gatk written 4 weeks ago by raf.marcondes • 20
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2
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176
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2
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Pararellization in GATK 4
haplotypecaller gatk multi-threading written 5 weeks ago by raf.marcondes • 20
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92
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1
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Combine samples in bam/vcf
gatk written 5 weeks ago by vctrm67 • 10 • updated 5 weeks ago by Pierre Lindenbaum ♦ 124k
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1
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86
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1
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Error when unzipping .gz files from GATK?
gatk written 5 weeks ago by vctrm67 • 10 • updated 5 weeks ago by RamRS ♦ 24k
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79
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Normal sample variant calling method without PON ?
gatk wes mutect2 sequencing written 5 weeks ago by Igor Islanov • 0
1
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1
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128
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1
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GATK Best Practices HaplotypeCaller Multi-sample Error
haplotypecaller gatk written 6 weeks ago by vctrm67 • 10
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1
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145
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1
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Extracting specific SNPs from VCF
vcf gatk snp written 7 weeks ago by igor • 0 • updated 7 weeks ago by Kevin Blighe ♦ 51k
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Reducing block size used in Spark versions of GATK tools
gatk dna block size spark written 10 weeks ago by aalith • 10 • updated 7 weeks ago by Biostar ♦♦ 20
1
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1
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205
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1
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HaplotypeCallerSpark How to use
gatk snp written 9 weeks ago by nanoide • 30 • updated 7 weeks ago by lakhujanivijay ♦ 4.6k
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298
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1
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Parsing through VCF annotated by Funcotator
vcf gatk annotated funcotator written 4 months ago by abbysue • 10 • updated 8 weeks ago by jonnsmith • 0
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How to handle allosomes and chrM in GATK?
gatk chrm snp wgs written 10 weeks ago by arup • 1.9k
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BwaMemIndexImageCreator fails to generate reference.img file
gatk reference genome index written 12 weeks ago by fmail1221 • 0 • updated 9 weeks ago by 7ehuang • 0
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