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<prev • 715 results • page 1 of 24 • next >
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Determining ploidy via read ratios with HaplotypeCaller: skewed results?
gatk ploidy illumina snp R written 2.8 years ago by mmats010 • 60 • updated 2 days ago by Biostar ♦♦ 20
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GATK FilterMutectCalls parameter max germline posterior ?
gatk threshold tool mutect2 written 3 days ago by jackyen • 0 • updated 3 days ago by ATpoint ♦ 21k
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why there is 0/0 genotyp in VCF file?
vcf gatk variant written 5 days ago by star • 190
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Job: Scientific writer for GATK at Broad Institute Data Sciences Platform
gatk job written 6 days ago by vdauwera • 950
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Processing WES mouse data using GATK on Terra Bio
terra gatk exome mm9 firecloud written 7 days ago by Arko • 20
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58
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Why invariant blocks in GATK consistently have very low quality scores (but not variant sites)
variant calling gatk snp written 12 days ago by yixianshuiesuan • 0
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95
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Vcf produced after ApplyVSQR step
gatk applyvsqr written 13 days ago by BAGeno • 140 • updated 13 days ago by andrew.j.skelton73 ♦ 5.8k
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1
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GATK VariantFiltration NumberFormatException
gatk variantfiltration numberformatexception written 16 days ago by ajaypaulsharma • 0 • updated 16 days ago by Brice Sarver • 2.8k
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90
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Analysis of exome samples build from different exome kits
exome gatk interval written 17 days ago by Nicolas Rosewick ♦ 8.0k • updated 17 days ago by andrew.j.skelton73 ♦ 5.8k
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Can Mutect2 be used for paper?
gatk mutect2 written 18 days ago by Laven9 • 0 • updated 18 days ago by Nicolas Rosewick ♦ 8.0k
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GATK multi sample variant calling
variant calling gatk snp written 18 days ago by cetin.m • 30
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13 follow
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Can You Please Tell Me Where I Find Information About .Fai File Format?
maf gatk written 9.2 years ago by Biomed ♦ 4.5k • updated 20 days ago by John Marshall ♦ 1.7k
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random selection of multi-sample vcf does not work
selectvariants gatk selectrandomfraction written 21 days ago by mernster • 0 • updated 21 days ago by finswimmer ♦ 12k
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5 follow
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Pipe SamToFastq, BWA mem not working
gatk sam bwa pipe written 4 weeks ago by abbysue • 10 • updated 22 days ago by Biostar ♦♦ 20
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What is the different if I call germline SNP/Indel with mutect and HaplotypeCaller?
gatk mutect haplotypecaller. written 24 days ago by Timze W • 20
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NA12878 High Confidence Callset Sequence Dictionaries
genome vcf alignment tool gatk written 24 days ago by ilee66 • 0 • updated 24 days ago by ATpoint ♦ 21k
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1
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User error while using GATK SplitNcigarReads
gatk written 4 weeks ago by jahanzaib119311 • 0
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13 follow
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BQSR: when it is applicable?
gatk bqsr base quality written 22 months ago by lamteva.vera • 160 • updated 25 days ago by demolidd77 • 40
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97
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Error in GATK BaseRecalibrator arguments
assembly gatk written 27 days ago by manubiomed20 • 0
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VQSRTranche filters in GATK
gatk next-gen snp written 19 months ago by anu014 • 170 • updated 27 days ago by nawar82 • 0
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getting different value list from GATK gc content and CANOES
gatk canoes cnv written 28 days ago by a.tavallaie • 0
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GATK RevertSamSpark No Max_Discard_Fraction option
gatk sam written 4 weeks ago by aalith • 0
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102
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Empty output of allele specific expression analysis by GATK
gatk ase rna-seq wgs written 4 weeks ago by F • 3.4k • updated 4 weeks ago by RamRS ♦ 23k
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139
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GATK SplitNCigarReads Error
gatk variant rna-seq written 4 weeks ago by BAGeno • 140
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Parsing through VCF annotated by Funcotator
vcf gatk annotated funcotator written 5 weeks ago by abbysue • 10
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Bowtie2 hg19 reference for gatk MuTect
gatk bowtie2 written 5 weeks ago by varsha619 • 80 • updated 5 weeks ago by h.mon ♦ 26k
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Calculate mean_GQ value from individual GQ values in a multi-sample VCF file
vcf gatk next-gen variant-calling sequencing written 2.4 years ago by aham • 40 • updated 6 weeks ago by jalinir • 0
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1
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160
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Struggling to use the GATK HaplotypeCaller on my bam files.
haplotypecaller gatk software error written 7 weeks ago by alhamidi.reem • 10
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GATK -Xmx4G and -Xmx8G
haplotypecaller gatk bioinformatics written 6 weeks ago by alhamidi.reem • 10 • updated 6 weeks ago by andrew.j.skelton73 ♦ 5.8k
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Removing the tagged variants after variant filtration step
gatk snp written 7 weeks ago by Satyajeet Khare • 1.4k
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