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2
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1
answer
150
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1
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Problem succesfully running freebayes
vcf fasta freebayes written 14 days ago by ja4123 • 0
3
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1
answer
72
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1
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File not suitable for fasta index generation.
fasta freebayes index written 14 days ago by ja4123 • 0 • updated 14 days ago by Pierre Lindenbaum ♦ 125k
4
votes
1
answer
130
views
1
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Unable to find FASTA index entry for '1'
fasta vcf bam freebayes written 6 weeks ago by ja4123 • 0
0
votes
1
answer
174
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1
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How to filter SNP and Indel under these criteria?
indel vcffilter freebayes vcftools snp written 9 weeks ago by r00628112 • 10 • updated 18 days ago by devarora • 40
0
votes
0
answers
108
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0
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Segmentation fault Freebayes
freebayes snp error segmentation written 8 weeks ago by luzglongoria • 40
1
vote
1
answer
83
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1
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Variant using freebayes
tetraploid genome freebayes 10x genomics written 10 weeks ago by nadiabeg.comsats • 0 • updated 10 weeks ago by colindaven • 1.9k
0
votes
1
answer
134
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1
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How to subset bamfile based on chromosome IDs
bam freebayes subset written 3 months ago by mernster • 0 • updated 3 months ago by ATpoint ♦ 28k
1
vote
1
answer
253
views
1
answer
Freebayes haplotype calling
variantcall haplotype freebayes snp written 6 months ago by k.itokawa • 0 • updated 6 months ago by colindaven • 1.9k
0
votes
1
answer
257
views
1
answer
Filter out low coverage and minor alleles of a frequency above 40%.
vcf variant calling freebayes hiv written 6 months ago by pennakiza • 50 • updated 6 months ago by bari.ballew • 190
1
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0
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188
views
0
answers
Test Freebayes on sample files
variant calling freebayes sequencing written 8 months ago by Bella_p • 50
1
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0
answers
255
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0
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Variant discrepancy between technical replicates
alignment freebayes written 8 months ago by kspata • 70 • updated 8 months ago by geek_y ♦ 10k
5
votes
1
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1.2k
views
1
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how to run freebayes in multi-thread
vcf multi-thread freebayes written 11 months ago by marongiu.luigi • 450 • updated 11 months ago by RamRS ♦ 25k
1
vote
1
answer
569
views
1
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Consensus VCF file from several variant callers
vcf variant calling freebayes gatk written 13 months ago by ajuiwl • 30 • updated 13 months ago by Pierre Lindenbaum ♦ 125k
0
votes
0
answers
521
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0
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Using freebayes to call variants
next-gen freebayes sequencing written 13 months ago by zhou_1228 • 0 • updated 13 months ago by finswimmer ♦ 13k
3
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1
answer
778
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1
answer
Freebayes outputs only one individual out of many
freebayes written 14 months ago by Fedster • 30
1
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1
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1.8k
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1
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SNP calling from pool sequencing with freebayes
ngs freebayes snp written 4.6 years ago by marcoabbestia • 0 • updated 16 months ago by Biostar ♦♦ 20
1
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1
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1.3k
views
1
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freebayes: changing min-coverage setting and still getting same size file output
freebayes min-coverage written 3.9 years ago by laurenvw • 20 • updated 16 months ago by RamRS ♦ 25k
5
votes
1
answer
779
views
1
answer
How to know if a variant is sequencing or mapping artifact?
vcf variant freebayes written 19 months ago by kspata • 70 • updated 19 months ago by finswimmer ♦ 13k
2
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0
answers
416
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0
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Freebayes command stopped due to lack of space
snp calling freebayes forum written 19 months ago by amcheroo • 0 • updated 19 months ago by finswimmer ♦ 13k
1
vote
1
answer
583
views
1
answer
Find variants supported by at least 20 reads freebayes
variant calling freebayes written 19 months ago by kspata • 70 • updated 19 months ago by finswimmer ♦ 13k
1
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0
answers
1.2k
views
0
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What do the freebayes parameters --pooled-continuous/--pooled-discrete mean?
variant-calling next-gen freebayes snp written 20 months ago by markd • 20
4
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0
answers
2.3k
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5 follow
0
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Getting Haplotypes from a VCF file
vcf haplotypes freebayes written 23 months ago by gkuffel22 • 70 • updated 22 months ago by Biostar ♦♦ 20
0
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0
answers
615
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0
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How to shorten runtimes of freebayes on very deep long reads with a smattering of largish indels
bam freebayes written 22 months ago by rleach • 120
11
votes
1
answer
2.9k
views
1
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Variant Calls: Freebayes vs GATK
.vcf gatk freebayes written 22 months ago by oars • 160 • updated 22 months ago by vdauwera • 960
0
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1
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2.2k
views
1
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freebayes haplotype calling (phased variants)
freebayes haplotype phase variant phased written 3.8 years ago by mark.rose • 30 • updated 23 months ago by gkuffel22 • 70
0
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1
answer
634
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1
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How unphased VCF is converted into ped file?
vcf ddrad phaseing freebayes ped written 24 months ago by jingjin2203 • 40 • updated 24 months ago by Kevin Blighe ♦ 53k
0
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1
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838
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1
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how to genotype given SNP alleles from NGS data using freebayes
ngs freebayes genotype written 2.3 years ago by J.F.Jiang • 760 • updated 2.1 years ago by ines.sanchezdonoso • 0
3
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0
answers
699
views
0
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Variant caller comparison for non-human data (highly varied populations)
variant calling gatk freebayes platypus genotyping written 2.2 years ago by hermathena • 40
4
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2
answers
1.6k
views
2
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Converting MNP to SNP
vcf freebayes snp written 2.3 years ago by finswimmer ♦ 13k
0
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0
answers
875
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0
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freebayes VCF output (FREQ header)
vcf freebayes written 2.3 years ago by Thomas Bradley • 90
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