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<prev • 38 results • page 1 of 2 • next >
1
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329
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sample order of the freebayes vcf output
vcf wes freebayes written 13 days ago by tangming2005 • 2.1k
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142
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Freebayes to output BAM after haplotype assembly
freebayes written 5 weeks ago by cvniru • 0 • updated 16 days ago by Biostar ♦♦ 20
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171
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What makes low frequency variants callers good at what they do?
variant calling lofreq freebayes somatic mutation written 7 weeks ago by CY • 30
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1
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200
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Calling SNPs with samtools: how to specify how many supporting observations are required?
variant calling samtools snps freebayes written 3 months ago by Lina F • 100 • updated 3 months ago by Brian Bushnell ♦ 13k
3
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1
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201
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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 4 months ago by Lauren • 10 • updated 4 months ago by Pierre Lindenbaum ♦ 96k
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573
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calling phased variants
phase variants freebayes problem platypus written 16 months ago by mark.rose • 10 • updated 4 months ago by arezansoff • 10
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232
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Is it necessery to perform GATK-BQSR before performing variant calling using freebayes.
gatk bqsr freebayes written 5 months ago by sktbanerjee1 • 20 • updated 5 months ago by finswimmer • 360
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1
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303
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1
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calculating genotype quality from genotype likelihood
genotype likelihood genotype quality freebayes written 5 months ago by Ana • 20 • updated 5 months ago by youcai • 20
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1
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1.0k
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1
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Detecting Variants near repeats
vcf repeats bam freebayes written 3.3 years ago by Adrian Pelin • 2.0k • updated 5 months ago by Macspider • 1.2k
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1
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302
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1
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How to fix FreeBayes error "unable to find FASTA index entry"
galaxy freebayes written 5 months ago by genome21 • 0 • updated 5 months ago by shenwei356 • 3.2k
1
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0
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309
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0
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CombineGVCFs + GenotypeGVCFs for Freebayes gVCF files?
freebayes gvcf written 5 months ago by William • 3.9k
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252
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complex indel precludes detection of overlapping SNPs
variant-calling pooled sample freebayes written 5 months ago by harold.smith.tarheel • 3.7k
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1
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388
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1
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varscan misses alternate variant alleles
variant freebayes insertion mpileup deletion written 9 months ago by mark.rose • 10
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297
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FreeBayes does not deal with ambiguous nucleotides -- what are good alternatives?
freebayes open source snp written 9 months ago by Lina F • 100
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381
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Underestimating heterozygotes in variant calling in FreeBayes
variant calling next-gen freebayes snp written 10 months ago by crossman.ca • 0
2
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1
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679
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1
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Freebayes tumor vs. normal inquiry
ngs tumor freebayes snp written 15 months ago by alons • 220 • updated 11 months ago by sambrightman • 20
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0
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459
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0
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FreeBayes Variant Calling Runtime
variant calling exome freebayes written 12 months ago by vhf_to_uhf • 0
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450
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Variant Calling output problem GL000 contigs
vardict freebayes mutect varscan written 16 months ago by morovatunc • 360
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0
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931
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freebayes haplotype calling (phased variants)
freebayes haplotype phase variant phased written 17 months ago by mark.rose • 10 • updated 17 months ago by geek_y ♦ 7.8k
0
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1
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825
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1
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Freebayes Variant calling
ngs freebayes written 17 months ago by manojkumarbioinfo • 20 • updated 17 months ago by bedeabc • 110
1
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1
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593
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1
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freebayes: changing min-coverage setting and still getting same size file output
freebayes min-coverage written 18 months ago by laurenvw • 10 • updated 18 months ago by apelin20 • 460
1
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471
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Freebayes variant calling: argument for min alternate total (by fraction)
freebayes min alt alleles written 18 months ago by laurenvw • 10
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2.7k
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FreeBayes vs GATK's HaplotypeCaller
vcf gatk quality freebayes variant caller written 19 months ago by Hatem Elshazly • 50 • updated 19 months ago by Carlos Borroto • 1.5k
4
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1
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681
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1
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Generate two haplotypes from bam and vcf
vcf gatk freebayes snp written 20 months ago by geek_y ♦ 7.8k
3
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2
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788
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2
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calling variants between two strains
samtools freebayes vcftools snp written 21 months ago by steven.lin.pur • 10 • updated 21 months ago by apelin20 • 460
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2
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3.1k
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Do freeBayes and platypus support gVCF (ie incremental variant calling for large sets of genomes)
freebayes platypus gvcf written 2.9 years ago by William • 3.9k
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how to add QualityOfDepth(QD) annotation to freebayes vcf
vcf qualitybydepth freebayes written 24 months ago by William • 3.9k • updated 23 months ago by Sean Davis ♦ 23k
2
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0
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710
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Variant Calling accounting for ALT contigs
variant calling gatk freebayes alt contig written 2.0 years ago by Benilton Carvalho • 20 • updated 2.0 years ago by Biostar ♦♦ 20
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How does FreeBayes evaluates variants that did not meet the --min-alternate-count (-C) and --min-alternate-fraction (-F) criteria?
freebayes snp written 2.3 years ago by Joanne Lim • 20 • updated 2.1 years ago by SNPsaurus • 40
3
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1
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1.3k
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1
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Lower GATK's HaplotypeCaller threshold for allele frequency as part of variant calling pipeline
vcf gatk ngs freebayes variant calling written 2.1 years ago by alons • 220
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