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How to generate the contigs ploidy priors table (yeast) for GATK DetermineGermlineContigPloidy --contig-ploidy-priors option ?
variant-calling gatk cnv gcnv written 18 days ago by mikizu • 0
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102
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Error while running vcf2maf tool
variant-calling maf vep vcf2maf vcfs written 9 weeks ago by Jordan • 1.1k
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1
answer
235
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1
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Creating a panel of normal from one normal sample
variant-calling gatk mutect2 panelofnormals written 8 months ago by Jordan • 1.1k • updated 8 months ago by Kevin Blighe ♦ 63k
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2
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9.9k
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6 follow
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What does BAF mean?
variant-calling baf written 3.2 years ago by Brian Bushnell ♦ 17k • updated 8 months ago by Fernado Perez-Villatoro • 0
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424
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1
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Variant calling pacbio bacteria
variant-calling sniffles bacteria pacbio pbsv written 12 months ago by rmf • 950 • updated 10 months ago by wrowell • 0
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1
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Calculating effective coverage/callable genome for variant calling from a bam file
genome variant-calling bam bigwig coverage written 12 months ago by Rubal • 330 • updated 12 months ago by Pierre Lindenbaum ♦ 129k
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1
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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 3.4 years ago by aham • 40 • updated 13 months ago by jalinir • 0
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1
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345
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Remove variants that do not map to human genome
vcf variant-calling qc written 15 months ago by john.michel.rouhana • 10 • updated 15 months ago by Pierre Lindenbaum ♦ 129k
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5 follow
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Genotyping diploid organisms from Sanger AB1 files
variant-calling sanger written 16 months ago by ognjen011 • 200 • updated 16 months ago by trausch • 1.5k
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5 follow
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Errors With Apt-Get When Attempting To Install Somaticsniper
variant-calling written 7.4 years ago by N • 10 • updated 18 months ago by Biostar ♦♦ 20
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5
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19 follow
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Combining Data Of Multiple Vcfs Into One.
vcf variant-calling written 7.2 years ago by Sheila • 320 • updated 18 months ago by Shicheng Guo • 8.3k
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7 follow
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Why is 0/0 homozygous reference call in VCF useful information?
vcf variant-calling sequencing written 21 months ago by lillian.thistlethwaite • 40 • updated 20 months ago by Biostar ♦♦ 20
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why and how multi allele gets reported during variant calling in vcf
variant-calling vcf allele snp multi-allele written 22 months ago by genie66 • 20
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0
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Using GIAB exome data to test targetome variant-calling pipeline
variant-calling whole-exome targetome giab written 4.5 years ago by Floydian_slip • 130 • updated 22 months ago by RamRS ♦ 28k
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1
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7 follow
1
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Keep Format and Individual fields when annotating VCF with VEP
vcf annotation vep variant-calling written 2.3 years ago by jsneaththompson • 90 • updated 23 months ago by MasMarius • 10
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Why a true variant is not getting called by Haplotypecaller.
variant-calling haplotypecaller next-gen written 4.4 years ago by AshishKS • 10 • updated 2.1 years ago by Biostar ♦♦ 20
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What do the freebayes parameters --pooled-continuous/--pooled-discrete mean?
variant-calling next-gen freebayes snp written 2.2 years ago by markd • 20
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861
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1
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GATK: .ped vs .fam and missing values
variant-calling gatk snp written 2.4 years ago by rmf • 950 • updated 2.4 years ago by Kevin Blighe ♦ 63k
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1
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How To Phase Haplotypes In A Highly Polymorphic Genome
vcf variant-calling written 6.5 years ago by Adrian Pelin • 2.4k • updated 2.5 years ago by Biostar ♦♦ 20
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1
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7 follow
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Samtools: merge and mpileup vs mpileup alone for variant-calling with multiple BAM
variant-calling merge samtools mpileup snp written 3.5 years ago by Rob • 120 • updated 2.5 years ago by Biostar ♦♦ 20
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Regenotype vcf using some samples as reference
vcf variant-calling snp written 2.5 years ago by rmf • 950
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1
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1
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phasing SNPs with 3 siblings
variant-calling snp written 2.5 years ago by rmf • 950 • updated 2.5 years ago by Pierre Lindenbaum ♦ 129k
2
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1
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783
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1
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Identifying variants differing between control/treatment
variant-calling gatk indel snp written 2.6 years ago by rmf • 950 • updated 2.6 years ago by Pierre Lindenbaum ♦ 129k
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620
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1
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Genotype calls for a list of variable sites
variant-calling gatk genotype-calling written 2.8 years ago by Jautis • 290 • updated 2.8 years ago by Pierre Lindenbaum ♦ 129k
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1.3k
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complex indel precludes detection of overlapping SNPs
variant-calling pooled sample freebayes written 3.4 years ago by harold.smith.tarheel • 4.6k
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Next-Generation Sequecing And Quantitative Traits Association Study
variant-calling ngs sequencing written 6.5 years ago by sorento7 • 30 • updated 3.7 years ago by Biostar ♦♦ 20
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1
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Extract allele frequencies from VCF
variant-calling vcf crisp written 3.9 years ago by mufernando • 10 • updated 3.9 years ago by Noushin N • 580
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959
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1
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Coming with a result with many VCF files?
vcf variant-calling mutation-calling written 4.3 years ago by morovatunc • 460 • updated 4.2 years ago by Denise CS • 5.1k
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6
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15k
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11 follow
6
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Variant Calling With Bcftools Call
variant-calling bcftools samtools mpileup written 6.4 years ago by tayebwajb • 90 • updated 4.5 years ago by vladimir.kovacevic • 60
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1
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1.8k
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1
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Sensitivity of variant calling
variant-calling next-gen sequencing written 5.1 years ago by adny • 50 • updated 5.1 years ago by Len Trigg • 1.5k
<prev • 75 results • page 1 of 3 • next >
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