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<prev • 51 results • page 1 of 2 • next >
4
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1
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91
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1
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How to know if a variant is sequencing or mapping artifact?
vcf variant freebayes written 9 hours ago by kspata • 30 • updated 4 hours ago by finswimmer ♦ 2.9k
2
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0
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68
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0
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Freebayes command stopped due to lack of space
snp calling freebayes forum written 10 days ago by amcheroo • 0 • updated 10 days ago by finswimmer ♦ 2.9k
1
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1
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71
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1
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Find variants supported by at least 20 reads freebayes
variant calling freebayes written 10 days ago by kspata • 30 • updated 10 days ago by finswimmer ♦ 2.9k
1
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0
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121
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0
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What do the freebayes parameters --pooled-continuous/--pooled-discrete mean?
variant-calling next-gen freebayes snp written 23 days ago by markd • 20
2
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0
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349
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0
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Getting Haplotypes from a VCF file
vcf haplotypes freebayes written 4 months ago by gkuffel22 • 50 • updated 11 weeks ago by Biostar ♦♦ 20
0
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0
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114
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How to shorten runtimes of freebayes on very deep long reads with a smattering of largish indels
bam freebayes written 12 weeks ago by rleach • 40
9
votes
1
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433
views
1
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Variant Calls: Freebayes vs GATK
.vcf gatk freebayes written 3 months ago by oars • 110 • updated 12 weeks ago by vdauwera • 770
0
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1
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1.4k
views
1
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freebayes haplotype calling (phased variants)
freebayes haplotype phase variant phased written 2.3 years ago by mark.rose • 10 • updated 4 months ago by gkuffel22 • 50
0
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1
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237
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1
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How unphased VCF is converted into ped file?
vcf ddrad phaseing freebayes ped written 4 months ago by jingjin2203 • 0 • updated 4 months ago by Kevin Blighe ♦ 22k
0
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1
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345
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1
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how to genotype given SNP alleles from NGS data using freebayes
ngs freebayes genotype written 9 months ago by J.F.Jiang • 700 • updated 6 months ago by ines.sanchezdonoso • 0
3
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0
answers
306
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0
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Variant caller comparison for non-human data (highly varied populations)
variant calling gatk freebayes platypus genotyping written 7 months ago by hermathena • 40
2
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1
answer
450
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1
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Converting MNP to SNP
vcf freebayes snp written 8 months ago by finswimmer ♦ 2.9k
0
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0
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335
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0
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freebayes VCF output (FREQ header)
vcf freebayes written 8 months ago by Thomas • 90
1
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0
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562
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0
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How to filter SNPs after Freebayes, if at all, in a fungal haploid genome alignment?
freebayes snp filtering written 9 months ago by Lina F • 120
1
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1
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743
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1
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sample order of the freebayes vcf output
vcf wes freebayes written 10 months ago by Ming Tang • 2.3k
0
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0
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351
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0
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Freebayes to output BAM after haplotype assembly
freebayes written 11 months ago by cvniru • 0 • updated 10 months ago by Biostar ♦♦ 20
0
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0
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384
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0
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What makes low frequency variants callers good at what they do?
variant calling lofreq freebayes somatic mutation written 12 months ago by CY • 130
3
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1
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632
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1
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Calling SNPs with samtools: how to specify how many supporting observations are required?
variant calling samtools snps freebayes written 14 months ago by Lina F • 120 • updated 14 months ago by Brian Bushnell ♦ 15k
3
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1
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469
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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 14 months ago by Lauren • 20 • updated 14 months ago by Pierre Lindenbaum ♦ 108k
0
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0
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966
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calling phased variants
phase variants freebayes problem platypus written 2.2 years ago by mark.rose • 10 • updated 14 months ago by arezansoff • 10
2
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1
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607
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1
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Is it necessery to perform GATK-BQSR before performing variant calling using freebayes.
gatk bqsr freebayes written 15 months ago by sktbanerjee1 • 30 • updated 15 months ago by finswimmer ♦ 2.9k
0
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1
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717
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1
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calculating genotype quality from genotype likelihood
genotype likelihood genotype quality freebayes written 15 months ago by Ana • 100 • updated 15 months ago by youcai • 40
2
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1
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1.4k
views
1
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Detecting Variants near repeats
vcf repeats bam freebayes written 4.1 years ago by Adrian Pelin • 2.1k • updated 15 months ago by Macspider • 2.4k
0
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1
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937
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1
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How to fix FreeBayes error "unable to find FASTA index entry"
galaxy freebayes written 15 months ago by genome21 • 0 • updated 15 months ago by shenwei356 ♦ 3.8k
1
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0
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999
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0
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CombineGVCFs + GenotypeGVCFs for Freebayes gVCF files?
freebayes gvcf written 16 months ago by William • 4.2k
0
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0
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578
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0
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complex indel precludes detection of overlapping SNPs
variant-calling pooled sample freebayes written 16 months ago by harold.smith.tarheel • 4.1k
0
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1
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721
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1
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varscan misses alternate variant alleles
variant freebayes insertion mpileup deletion written 19 months ago by mark.rose • 10
0
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0
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568
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0
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FreeBayes does not deal with ambiguous nucleotides -- what are good alternatives?
freebayes open source snp written 19 months ago by Lina F • 120
0
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0
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735
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0
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Underestimating heterozygotes in variant calling in FreeBayes
variant calling next-gen freebayes snp written 21 months ago by crossman.ca • 0
2
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1
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1.2k
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1
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Freebayes tumor vs. normal inquiry
ngs tumor freebayes snp written 2.1 years ago by alons • 250 • updated 21 months ago by sambrightman • 20
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