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<prev • 51 results • page 1 of 2 • next >
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SNP calling from pool sequencing with freebayes
ngs freebayes snp written 3.2 years ago by marcoabbestia • 0 • updated 1 day ago by Biostar ♦♦ 20
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936
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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 2.6 years ago by laurenvw • 20 • updated 4 days ago by Ram ♦ 17k
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1
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214
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How to know if a variant is sequencing or mapping artifact?
vcf variant freebayes written 12 weeks ago by kspata • 30 • updated 12 weeks ago by finswimmer ♦ 5.3k
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128
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Freebayes command stopped due to lack of space
snp calling freebayes forum written 3 months ago by amcheroo • 0 • updated 3 months ago by finswimmer ♦ 5.3k
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146
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Find variants supported by at least 20 reads freebayes
variant calling freebayes written 3 months ago by kspata • 30 • updated 3 months ago by finswimmer ♦ 5.3k
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What do the freebayes parameters --pooled-continuous/--pooled-discrete mean?
variant-calling next-gen freebayes snp written 3 months ago by markd • 20
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608
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Getting Haplotypes from a VCF file
vcf haplotypes freebayes written 7 months ago by gkuffel22 • 50 • updated 5 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 5 months ago by rleach • 90
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1
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686
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1
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Variant Calls: Freebayes vs GATK
.vcf gatk freebayes written 5 months ago by oars • 150 • updated 5 months ago by vdauwera • 810
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freebayes haplotype calling (phased variants)
freebayes haplotype phase variant phased written 2.5 years ago by mark.rose • 20 • updated 7 months ago by gkuffel22 • 50
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1
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310
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How unphased VCF is converted into ped file?
vcf ddrad phaseing freebayes ped written 7 months ago by jingjin2203 • 0 • updated 7 months ago by Kevin Blighe ♦ 28k
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424
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how to genotype given SNP alleles from NGS data using freebayes
ngs freebayes genotype written 12 months ago by J.F.Jiang • 710 • updated 9 months ago by ines.sanchezdonoso • 0
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373
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Variant caller comparison for non-human data (highly varied populations)
variant calling gatk freebayes platypus genotyping written 10 months ago by hermathena • 40
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1
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604
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Converting MNP to SNP
vcf freebayes snp written 10 months ago by finswimmer ♦ 5.3k
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406
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freebayes VCF output (FREQ header)
vcf freebayes written 11 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 12 months ago by Lina F • 150
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877
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1
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sample order of the freebayes vcf output
vcf wes freebayes written 13 months ago by Ming Tang • 2.4k
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412
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Freebayes to output BAM after haplotype assembly
freebayes written 14 months ago by cvniru • 0 • updated 13 months ago by Biostar ♦♦ 20
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446
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What makes low frequency variants callers good at what they do?
variant calling lofreq freebayes somatic mutation written 14 months ago by CY • 190
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Calling SNPs with samtools: how to specify how many supporting observations are required?
variant calling samtools snps freebayes written 17 months ago by Lina F • 150 • updated 17 months ago by Brian Bushnell ♦ 15k
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Variant callers reporting different read depth on same alignment
variant calling gatk freebayes variant annotation written 17 months ago by Lauren • 20 • updated 17 months ago by Pierre Lindenbaum ♦ 112k
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calling phased variants
phase variants freebayes problem platypus written 2.5 years ago by mark.rose • 20 • updated 17 months ago by arezansoff • 20
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1
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710
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Is it necessery to perform GATK-BQSR before performing variant calling using freebayes.
gatk bqsr freebayes written 18 months ago by sktbanerjee1 • 30 • updated 18 months ago by finswimmer ♦ 5.3k
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833
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calculating genotype quality from genotype likelihood
genotype likelihood genotype quality freebayes written 18 months ago by Ana • 100 • updated 18 months ago by youcai • 40
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Detecting Variants near repeats
vcf repeats bam freebayes written 4.3 years ago by Adrian Pelin • 2.2k • updated 18 months ago by Macspider • 2.5k
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How to fix FreeBayes error "unable to find FASTA index entry"
galaxy freebayes written 18 months ago by genome21 • 0 • updated 18 months ago by shenwei356 ♦ 4.1k
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CombineGVCFs + GenotypeGVCFs for Freebayes gVCF files?
freebayes gvcf written 18 months ago by William • 4.3k
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680
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complex indel precludes detection of overlapping SNPs
variant-calling pooled sample freebayes written 18 months ago by harold.smith.tarheel • 4.2k
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850
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varscan misses alternate variant alleles
variant freebayes insertion mpileup deletion written 22 months ago by mark.rose • 20
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648
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FreeBayes does not deal with ambiguous nucleotides -- what are good alternatives?
freebayes open source snp written 22 months ago by Lina F • 150
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