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how to run freebayes in multi-thread
vcf multi-thread freebayes written 1 day ago by marongiu.luigi • 360
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Consensus VCF file from several variant callers
vcf variant calling freebayes gatk written 9 weeks ago by ajuiwl • 30 • updated 9 weeks ago by Pierre Lindenbaum ♦ 116k
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Using freebayes to call variants
next-gen freebayes sequencing written 10 weeks ago by zhou_1228 • 0 • updated 10 weeks ago by finswimmer ♦ 9.8k
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Freebayes outputs only one individual out of many
freebayes written 3 months ago by Fedster • 20
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SNP calling from pool sequencing with freebayes
ngs freebayes snp written 3.6 years ago by marcoabbestia • 0 • updated 5 months ago by Biostar ♦♦ 20
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freebayes: changing min-coverage setting and still getting same size file output
freebayes min-coverage written 3.0 years ago by laurenvw • 20 • updated 5 months ago by RamRS ♦ 20k
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How to know if a variant is sequencing or mapping artifact?
vcf variant freebayes written 7 months ago by kspata • 40 • updated 7 months ago by finswimmer ♦ 9.8k
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Freebayes command stopped due to lack of space
snp calling freebayes forum written 8 months ago by amcheroo • 0 • updated 8 months ago by finswimmer ♦ 9.8k
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Find variants supported by at least 20 reads freebayes
variant calling freebayes written 8 months ago by kspata • 40 • updated 8 months ago by finswimmer ♦ 9.8k
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What do the freebayes parameters --pooled-continuous/--pooled-discrete mean?
variant-calling next-gen freebayes snp written 8 months ago by markd • 20
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Getting Haplotypes from a VCF file
vcf haplotypes freebayes written 12 months ago by gkuffel22 • 70 • updated 10 months ago by Biostar ♦♦ 20
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How to shorten runtimes of freebayes on very deep long reads with a smattering of largish indels
bam freebayes written 10 months ago by rleach • 90
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Variant Calls: Freebayes vs GATK
.vcf gatk freebayes written 10 months ago by oars • 150 • updated 10 months ago by vdauwera • 890
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freebayes haplotype calling (phased variants)
freebayes haplotype phase variant phased written 2.9 years ago by mark.rose • 30 • updated 12 months ago by gkuffel22 • 70
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How unphased VCF is converted into ped file?
vcf ddrad phaseing freebayes ped written 12 months ago by jingjin2203 • 0 • updated 12 months ago by Kevin Blighe ♦ 37k
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how to genotype given SNP alleles from NGS data using freebayes
ngs freebayes genotype written 17 months ago by J.F.Jiang • 730 • updated 14 months ago by ines.sanchezdonoso • 0
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Variant caller comparison for non-human data (highly varied populations)
variant calling gatk freebayes platypus genotyping written 15 months ago by hermathena • 40
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Converting MNP to SNP
vcf freebayes snp written 15 months ago by finswimmer ♦ 9.8k
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freebayes VCF output (FREQ header)
vcf freebayes written 16 months ago by Thomas • 90
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How to filter SNPs after Freebayes, if at all, in a fungal haploid genome alignment?
freebayes snp filtering written 17 months ago by Lina F • 150
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sample order of the freebayes vcf output
vcf wes freebayes written 18 months ago by Ming Tang • 2.4k
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Freebayes to output BAM after haplotype assembly
freebayes written 19 months ago by cvniru • 0 • updated 18 months ago by Biostar ♦♦ 20
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What makes low frequency variants callers good at what they do?
variant calling lofreq freebayes somatic mutation written 19 months ago by CY • 270
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Calling SNPs with samtools: how to specify how many supporting observations are required?
variant calling samtools snps freebayes written 22 months ago by Lina F • 150 • updated 22 months ago by Brian Bushnell ♦ 16k
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Variant callers reporting different read depth on same alignment
variant calling gatk freebayes variant annotation written 22 months ago by Lauren • 30 • updated 22 months ago by Pierre Lindenbaum ♦ 116k
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calling phased variants
phase variants freebayes problem platypus written 2.9 years ago by mark.rose • 30 • updated 22 months ago by arezansoff • 20
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Is it necessery to perform GATK-BQSR before performing variant calling using freebayes.
gatk bqsr freebayes written 23 months ago by sktbanerjee1 • 30 • updated 23 months ago by finswimmer ♦ 9.8k
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calculating genotype quality from genotype likelihood
genotype likelihood genotype quality freebayes written 23 months ago by Ana • 130 • updated 23 months ago by youcai • 40
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Detecting Variants near repeats
vcf repeats bam freebayes written 4.7 years ago by Adrian Pelin • 2.2k • updated 23 months ago by Macspider • 2.7k
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How to fix FreeBayes error "unable to find FASTA index entry"
galaxy freebayes written 23 months ago by genome21 • 10 • updated 23 months ago by shenwei356 ♦ 4.5k
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