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--max-alleles argument not recognized
vcftools snp written 5.5 years ago by boris • 0 • updated 9 days ago by Biostar ♦♦ 20
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1
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171
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1
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vcftools --fst-window- problems
fst-window vcftools written 6 weeks ago by florycamacho305 • 0 • updated 28 days ago by fu_entomology • 20
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135
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Identifying Private SNPs between multi sample vcf files.
bcftools bcftools isec vcftools vcf-compare written 4 weeks ago by nataliagru1 • 50
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170
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To remove variants that encode for PE-PPE proteins from .vcf file
bedtools annovar vcftools written 8 weeks ago by kumari.indu31 • 0
2
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1
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153
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1
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VCF tools --freq output file
vcftools allelefrequency fileformat written 9 weeks ago by Inquisitive8995 • 170 • updated 9 weeks ago by Kevin Blighe ♦ 65k
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1
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150
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1
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vcftools discrepancy in mean depth values per site
vcf depth coverage snp vcftools written 11 weeks ago by oscarmirap • 10 • updated 11 weeks ago by Kevin Blighe ♦ 65k
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1
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142
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1
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Vcftools order of operations for filtering?
genome vcftools snp written 3 months ago by aj • 0 • updated 3 months ago by Pierre Lindenbaum ♦ 130k
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1
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131
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1
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extracting SNPs from .vcf file along with CHR and POS
vcftools written 3 months ago by anamaria • 100
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1
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197
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1
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How to filter a VCF file with a list of CHR or contig IDs?
vcf chromosome contigs vcftools awk written 3 months ago by lexic2713 • 10 • updated 3 months ago by drkennetz • 500
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From VCF, create only .tfam file
vcf vcftools tped tfam plink written 4.6 years ago by mpauper • 20 • updated 3 months ago by chrchang523 ♦ 7.3k
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164
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Vcf filtering GT for between sample variants only
vcf heterozygous vcftools snp written 3 months ago by kadamek49 • 0
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4
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26k
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5 follow
4
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Help On Merging Vcf Files By Using Vcftools
vcf merge vcftools written 9.7 years ago by Jianfengmao • 310 • updated 3 months ago by Biostar ♦♦ 20
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159
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Relatedness check for trio samples (Proband/Parents)
vcf relatedness next-gen vcftools snp written 4 months ago by kaur.supan13 • 0
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179
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1
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remove listed singletons from vcftools output
genome next-gen vcftools sequencing written 4 months ago by QPaps04 • 0
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144
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0
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Filter SNPs for DP using mean + 2*SD
filter next-gen vcftools snp depth written 4 months ago by QPaps04 • 0
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2
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2.1k
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2
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Split a large VCF into user defined regions
vcf vcftools sequencing written 4.0 years ago by zelia.worman • 0 • updated 6 months ago by nmzt43 • 0
0
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1
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217
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1
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How to pass a variable to vcftools --weir-fst-pop
fst vcftools bash written 6 months ago by gary.napier • 20
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1
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270
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1
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Filtering VCF file by INFO flag
vcf vcftools written 7 months ago by zhamouda • 0
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3
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5.4k
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8 follow
3
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SnpMatrix from VCF file
vcf matrixeqtl snpmatrix vcftools eqtl written 3.5 years ago by Dhana • 80 • updated 7 months ago by cannilay • 20
2
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2
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271
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2
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vcftools separate only selected chrom allocation from 4gb vcf file
vcf filter allocation vcftools written 8 months ago by dev.info.2021 • 0
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1
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502
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1
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How to filter SNP and Indel under these criteria?
indel vcffilter freebayes vcftools snp written 10 months ago by r00628112 • 10 • updated 8 months ago by devarora • 230
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246
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bcftools error when re-annotating the FILTER column of a VCF when multiple ";" delimited FILTER values exist
vcf bcftools vcftools written 8 months ago by curious • 430
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246
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0
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How to calculate linkage disequilibrium (LD) with only two genomes?
linkage disequilibrium plink ld vcftools written 9 months ago by KL_STKLBK • 0
1
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434
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0
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vcftools not ouputting log file when run from perl
vcf vcftools written 9 months ago by dec986 • 230
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1
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192
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1
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VCFTools Removing Individuals and SNP counting
vcftools snp written 9 months ago by adnichols • 0 • updated 9 months ago by inedraylig • 20
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1
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348
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1
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Require Genotypes In Vcf File In Order To Output Frequency Statistics
vcf allele frequency vcftools af written 9 months ago by ja4123 • 0
1
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438
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0
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Why is VCFTools excluding so many SNPs in its Tajima D calculation?
vcftools snp population genetics written 10 months ago by Ace • 70 • updated 9 months ago by Biostar ♦♦ 20
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908
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vcftools Tajima's D calculation
vcftools tajimasd selection written 9 months ago by biogirl • 190
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275
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0
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Error with bcftools and vcftools and removing individuals
vcf bcftools vcftools written 9 months ago by seta • 1.3k
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1.7k
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5 follow
0
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Calculate Fis (inbreeding coefficient)
vcftools snp written 14 months ago by mostafarafiepour • 80 • updated 10 months ago by ginushika • 0
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