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Are there any issues with using sample reads coming from different technologies and having different depths to do joint variant calling (gatk)?
variant calling gatk hiseq snp novaseq written 1 day ago by serpalma.v • 30 • updated 3 hours ago by bari.ballew • 200
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Which of the 4 SureSelect Agilent BED files to use with GATK haplotype caller?
variant calling gatk sureselect written 1 day ago by curious • 210
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Merge VCF file
vcf gatk pca gwas written 2 days ago by devarora • 50 • updated 2 days ago by Pierre Lindenbaum ♦ 126k
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What Agilent Interval Files (.Bed) Should I Use For Exome Variant Calling With Gatk?
agilent bed gatk written 6.2 years ago by newDNASeqer • 670 • updated 2 days ago by Karma • 270
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How to caracterize single point mutation (or editing) in RNAseq?
rnaseq gatk written 2 days ago by silas008 • 100
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47
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Failed to find GenomeAnalysisTKLite.jar file
seqmule gatklite gatk written 3 days ago by bioinformatics98 • 0
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361
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GATK GermlineCNVCaller & PostprocessGermlineCNVCalls
software error gatk cnv written 9 months ago by rajitz • 20 • updated 5 days ago by Z-F • 10
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53
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Difference in .bed target region base count and mapped base count for different tools
software gatk samtools tool written 6 days ago by gavehan • 0
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60
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GATK UnifiedGenotyper Stuck at "Preparing for traversal over 1 BAM files|"
unifiedgenotyper gatk snpcalling indelrealigner written 7 days ago by sevvalakturk96 • 0 • updated 7 days ago by Pierre Lindenbaum ♦ 126k
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read group, fastq files, and multiple run ids
picard gatk fastq next-gen readgroups written 9 days ago by Cricket • 10
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99
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GATK4, BaseRecalibrator, Known site, Drosophila
gene alignment sequence snp gatk written 21 days ago by wjddn216 • 10
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43
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Scatter / Gather for BaseRecalibrator on a single human WES dataset?
exome gatk next-gen human bqsr written 14 days ago by asg • 0
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BQSR BD/BI Tags into integer values?
gatk bqsr written 8 weeks ago by QVINTVS_FABIVS_MAXIMVS • 2.3k • updated 17 days ago by Biostar ♦♦ 20
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Validating Predictions Of Small Insertions / Deletions
gatk variant written 6.0 years ago by Ron • 990 • updated 25 days ago by Biostar ♦♦ 20
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81
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break_blocks & GATK switch REF & ALT alleles
vcf gatk written 26 days ago by dec986 • 210
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534
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GATK HaplotypeCaller Problems
software error gatk next-gen alignment written 11 months ago by chengye • 10 • updated 28 days ago by Biostar ♦♦ 20
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84
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GATK's NuMT detection algorithm?
variant calling gatk mitochondria written 29 days ago by a.j.wilson0000 • 10
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87
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BaseRecalibrator takes forever to run. Any suggestions?
gatk whole exome written 29 days ago by khorms • 50
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GATK CNV Pipeline not plotting all discovered segments - PlotModeledSegments
gatk cnv written 4 weeks ago by taylor.falk3 • 0 • updated 4 weeks ago by genomax ♦ 78k
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Tools to filter the heterozygous SNPs with biased allele depth (AD) values in vcf file.
vcf gatk allele depth ad heterozygous snps written 5 weeks ago by rimgubaev • 180 • updated 5 weeks ago by harold.smith.tarheel • 4.5k
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Validating pre-processing pipeline from FASTQ to BAM
gatk picard samtools written 5 weeks ago by Maxime • 0
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Heterozygous calls (SNPs) problem while working with inbred lines.
vcf snps gatk heterozygous sequencing errors written 5 weeks ago by rimgubaev • 180
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101
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Fisher strand (FS) 0?
fs gatk fisher strand written 5 weeks ago by JM • 0 • updated 5 weeks ago by finswimmer ♦ 13k
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81
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Eliminating panel mutations based on coverage of PoN
gatk filtering written 5 weeks ago by vctrm67 • 10
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5 follow
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Computational resources for WGS variant calling
variant calling wgs bwakit openstack gatk written 11 weeks ago by alesssia • 560 • updated 5 weeks ago by Jeremy Leipzig ♦ 19k
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182
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6 follow
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Building Dict File for GATK
gatk java written 5 weeks ago by dec986 • 210 • updated 5 weeks ago by Karma • 270
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2
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336
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Somatic variant calling mutect2 tumour only
gatk snp mutect2 written 11 weeks ago by cellulebioinfobiscem • 10 • updated 5 weeks ago by newbio17 • 80
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78
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VCF files never get annotated with PG tag for CalculateGenotypePosteriors
gatk calculategenotypeposteriors genotype denovo written 5 weeks ago by lait • 140
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82
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GATK BaseRecalibrator and platform?
gatk written 5 weeks ago by vctrm67 • 10
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82
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1
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GATK Indelrealignment Problem : The input is truncated?
gatk realignment eof marker written 6 weeks ago by sevvalakturk96 • 0 • updated 6 weeks ago by kanika.151 • 80
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