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SnpEff question for Variant annotation
gene vcf next-gen snpeff written 24 days ago by mandar.bedse • 0 • updated 24 days ago by Pierre Lindenbaum ♦ 124k
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144
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Ways to improve SnpEff prediction
snpeff snp written 6 weeks ago by Mohammed • 10 • updated 5 weeks ago by zx8754 ♦ 8.7k
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107
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GC overhead error [java.lang.OutOfMemoryError] while running snpEFF version 4.1
next-gen snpeff written 6 weeks ago by halo22 • 130
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4
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6 follow
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snpEff building new database ERROR
database snpeff new written 10 months ago by Anastasia A. • 0 • updated 10 weeks ago by arif.ashraf.opu • 10
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156
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SNPEff missing annotations from VCF?
vcf snpeff written 4 months ago by vctrm67 • 10
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220
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Custom database in snpEff (Bos taurus ARS-UCD1.2)
annotation snpeff snp written 4 months ago by Eli Korvigo • 160
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157
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snpEff Error - Stop progressing after Predicting variants
snpeff hg19 written 4 months ago by woojoy14 • 0
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237
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1
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snpEff: Fatal error reading file the input VCF files and stop runing
snpeff fetal error written 5 months ago by Shicheng Guo • 7.8k
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221
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snpEff for bacteria genome
snpeff written 6 months ago by maricom • 0
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275
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Linkage disequilibrium from multi-sample vcf file
vcf snpeff vcftools ld written 6 months ago by felipead66 • 40 • updated 6 months ago by RamRS ♦ 25k
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8 follow
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Is SNPeff still the standard for variant effect prediction?
exome annotation snpeff variant written 2.4 years ago by Lauren • 50 • updated 6 months ago by Shicheng Guo • 7.8k
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182
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SnpEff: How to match variants with line ID in 1001 Genomes Project?
snpeff snp sequencing written 6 months ago by chase.lewis • 40 • updated 6 months ago by zx8754 ♦ 8.7k
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193
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fasta sequences from snpeff output file
fasta snpeff written 6 months ago by felipead66 • 40
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222
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snpEff output gets zero results for synonymous SNPs
snpeff synonymous written 6 months ago by felipead66 • 40 • updated 6 months ago by finswimmer ♦ 13k
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Filter vcf file using coordinate of bed , the result is SnpSift had filtered some wrong items, why ?
snpsift vcf snpeff snp written 6 months ago by duolin1 • 10 • updated 6 months ago by zx8754 ♦ 8.7k
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270
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1
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SnpEff HGVS doesn't match to fields of ref and alt alleles
hgvs annotation snpeff snp variant annotation written 6 months ago by mariafirulevabio • 40
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240
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snpEff - ERROR_CHROMOSOME_NOT_FOUND
snpeff written 6 months ago by ar.satkhol18 • 0 • updated 6 months ago by WouterDeCoster ♦ 42k
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1
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241
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1
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Which reference genome for the annotation of the 1KG variant data by snpEff?
snpeff reference genome variant annotation written 6 months ago by Nam Le Quang • 70
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SnPEff ANN[*].FEATURE and ANN[*].FEATUREID annotation
structural_interaction_variant snpeff written 7 months ago by yasminsoareslima • 10 • updated 7 months ago by RamRS ♦ 25k
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1
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SNP annotation with R and SnpEff
R snpeff snp written 2.0 years ago by wpierrick • 80 • updated 7 months ago by zx8754 ♦ 8.7k
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306
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SnpEff START/STOP codon not found error
software error snpeff snp written 8 months ago by thomasbersez • 50 • updated 7 months ago by Biostar ♦♦ 20
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240
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Snpeff for predicting snp effect
snpeff snp written 7 months ago by manjumoorthy95 • 20
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2
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863
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6 follow
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Downstream analysis of VCF files obtained from VarScan2
vcf wes snpeff varscan2 somatic variations written 12 months ago by Raheleh • 120 • updated 8 months ago by bari.ballew • 190
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390
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More general annotation using snpEff
genome annotation snpeff written 10 months ago by bwczech • 90
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Annotating Mycobacterium tuberculosis VCF file using snpEFF and aNNOVAR
annotation snpeff mtb snp annovar written 10 months ago by S AR • 50
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1
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511
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1
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several effect for one SNP annotated by SNPeff
annotation snpeff snp written 11 months ago by reza • 210
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1
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500
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1
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Annotate VCF on specific transcripts (ANN field)
vcf snpsift snpeff written 12 months ago by FGV • 110 • updated 12 months ago by Pierre Lindenbaum ♦ 124k
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1
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405
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Why snpEff annotation give different names to one same gene?
mtdna snpeff written 12 months ago by MatthewP • 320 • updated 12 months ago by jared.andrews07 • 4.1k
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Summary statistics of VCF annotated files (snpEff)
vcf annotation snpeff statistics written 13 months ago by bwczech • 90
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399
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"count"in the snpEFF html output
snpeff written 13 months ago by lifang5389 • 0
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