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Comment: C: How to do SNP selection in large VCF/BCF/GenotypeTables in R like you can using
6.1 years ago by William ★ 5.3k
0
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3.3k
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Comment: C: How to do SNP selection in large VCF/BCF/GenotypeTables in R like you can using
6.1 years ago by William ★ 5.3k
0
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1
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3.3k
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Comment: C: How to do SNP selection in large VCF/BCF/GenotypeTables in R like you can using
6.1 years ago by William ★ 5.3k
0
votes
1
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3.3k
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Comment: C: Sensitive (BLAST like) and fast alignment of millions of sequences against human
6.2 years ago by William ★ 5.3k
0
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1
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3.3k
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Comment: C: Sensitive (BLAST like) and fast alignment of millions of sequences against human
6.2 years ago by William ★ 5.3k
0
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0
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3.3k
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Comment: C: Sensitive (BLAST like) and fast alignment of millions of sequences against human
6.2 years ago by William ★ 5.3k
4
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11
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3.3k
views
Sensitive (BLAST like) and fast alignment of millions of sequences against human sized reference genomes
blast bwa alignment lift over multicopy
updated 6.2 years ago by 15k • written 6.2 years ago by ★ 5.3k
0
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1
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2.2k
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Comment: C: Should I use a bad/ mediocre gene model as input for STAR RNA-seq alignment?
6.3 years ago by William ★ 5.3k
5
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4
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2.2k
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Should I use a bad/ mediocre gene model as input for STAR RNA-seq alignment?
RNA-Seq star gene_model incremental
updated 6.3 years ago by 5.7k • written 6.3 years ago by ★ 5.3k
0
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1
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2.6k
views
Comment: C: How to display a VCF/BCF file or stream as a paginated table in a python web fra
6.5 years ago by William ★ 5.3k
3
votes
6
replies
2.6k
views
How to display a VCF/BCF file or stream as a paginated table in a python web framework (e.g. Django)?
vcf gui
updated 4 months ago by 22k • written 6.5 years ago by ★ 5.3k
0
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0
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2.6k
views
Comment: C: How to display a VCF/BCF file or stream as a paginated table in a python web fra
6.5 years ago by William ★ 5.3k
0
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3
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1.4k
views
How to do a local denovo assembly including unmapped paired reads for many samples to genotype a large insertion.
local assembly
updated 6.7 years ago by 35k • written 6.7 years ago by ★ 5.3k
0
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0
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2.3k
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Comment: C: Is it possible to use haplotypes instead of SNPs for association testing with ph
6.7 years ago by William ★ 5.3k
0
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0
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2.3k
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Comment: C: Is it possible to use haplotypes instead of SNPs for association testing with ph
6.7 years ago by William ★ 5.3k
2
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3
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2.3k
views
Is it possible to use haplotypes instead of SNPs for association testing with phenotypes?
SNP haplotypes gwas
updated 6.7 years ago by ▴ 670 • written 6.7 years ago by ★ 5.3k
0
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0
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3.6k
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Comment: C: Python library for parsing bcftools stats file
6.7 years ago by William ★ 5.3k
2
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2
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3.6k
views
Python library for parsing bcftools stats file
bcftools
6.7 years ago by William ★ 5.3k
0
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0
replies
3.9k
views
How to plot VCF missingness per sample (.imiss) and per variant (.lmiss) in python?
qc plink vcftools vcf
updated 6.8 years ago by 20 • written 7.2 years ago by ★ 5.3k
1
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0
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6.9k
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Answer: A: How to determine percentage missing genotypes in VCF/BCF?
6.8 years ago by William ★ 5.3k
1
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1
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4.6k
views
Expression data missing in a GEO study
GEO bioconductor GEOquery
updated 2.3 years ago by 43k • written 9.6 years ago by ★ 5.3k
0
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2
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1.9k
views
Can IonProton sequencing data be processed using BWA + FreeBayes or CLC?
ionproton
6.9 years ago by William ★ 5.3k
4
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1
reply
9.9k
views
Answer: A: GBS and RADseq
7.0 years ago by William ★ 5.3k
2
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2
replies
1.9k
views
Why do indel variants need a leading base according to the VCF spec?
vcf
updated 7.0 years ago by 43k • written 7.0 years ago by ★ 5.3k
0
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0
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6.4k
views
Answer: A: Does allele refer to the entire gene sequence or one position of the gene sequen
7.0 years ago by William ★ 5.3k
7
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4
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3.7k
views
Recent comparison of BWA-mem versus Berkeley SNAP aligner, TP, TN and speed.
snap bwa
updated 19 months ago by 43k • written 8.6 years ago by ★ 5.3k
16
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2
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44k
views
Answer: A: How to filter vcf file on minimum genotype depth and quality for each sample
7.1 years ago by William ★ 5.3k
35
votes
14
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44k
views
9 follow
How to filter vcf file on minimum genotype depth and quality for each sample
vcf bcftools
updated 7 months ago by ▴ 130 • written 7.8 years ago by ★ 5.3k
0
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0
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5.0k
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Comment: C: CombineGVCFs + GenotypeGVCFs for Freebayes gVCF files?
7.2 years ago by William ★ 5.3k
2
votes
1
reply
5.0k
views
CombineGVCFs + GenotypeGVCFs for Freebayes gVCF files?
freebayes gvcf
7.2 years ago by William ★ 5.3k
10
votes
7
replies
3.4k
views
Best visual and interactive genotype matrix (VCF) exploration tool
vcf bcftools interactive visual
updated 7.2 years ago by ▴ 360 • written 7.2 years ago by ★ 5.3k
0
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0
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1.6k
views
Comment: C: Senior Software Developer
7.2 years ago by William ★ 5.3k
3
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4
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2.9k
views
How to filter a VCF on a set of samples having genotypes containing the minor allele?
vcf bcftools snpsift
7.3 years ago by William ★ 5.3k
1
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0
replies
2.9k
views
Comment: C: How to filter a VCF on a set of samples having genotypes containing the minor al
7.3 years ago by William ★ 5.3k
0
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1
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2.9k
views
Comment: C: How to filter a VCF on a set of samples having genotypes containing the minor al
7.3 years ago by William ★ 5.3k
45
votes
9
replies
15k
views
7 follow
Best Genome Browser To Look At Structural Variation Calls
updated 7.3 years ago by ▴ 10 • written 11.7 years ago by ★ 5.3k
3
votes
1
reply
2.9k
views
How to run SnpEff for Tomato 2.5 (S_lycopersicum_chromosomes.2.50) reference, gff3 and VCF?
snpeff
updated 7.3 years ago by ★ 2.5k • written 7.3 years ago by ★ 5.3k
4
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1
reply
20k
views
Answer: A: Update 'ID' column in VCF file using BCFtools annotate
7.4 years ago by William ★ 5.3k
1
vote
1
reply
4.6k
views
Comment: C: Best tools for lifting over genome coordinates for non model organism (custom) r
7.4 years ago by William ★ 5.3k
2
votes
0
replies
2.3k
views
Recent comparison between variant effect prediction tools, mainly SnpEff v.s. Ensembl VEP
effect prediction
7.5 years ago by William ★ 5.3k
1
vote
1
reply
2.3k
views
Merge phased SNP variants to haplotypes? And is vcfallelicprimitives reversible?
vcf
updated 7.5 years ago by 20 • written 7.6 years ago by ★ 5.3k
2
votes
4
replies
4.2k
views
Cnvnator Genotype Regions Error : Can'T Find Bin 1000
updated 7.6 years ago by ▴ 10 • written 10.6 years ago by ★ 5.3k
1
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0
replies
2.0k
views
Answer: A: Vcf strange representation of alt and ref
7.7 years ago by William ★ 5.3k
0
votes
0
replies
2.0k
views
How does Plink (or any stats genetics tool) deal with missing genotypes in linear/logistic regression?
plink linear regression missing_genotypes
7.7 years ago by William ★ 5.3k
2
votes
0
replies
5.1k
views
Answer: A: how to analyze plot-vcfstats
7.8 years ago by William ★ 5.3k
1
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1
reply
2.9k
views
Answer: A: Insillico dual restriction enzyme reference genome digestion.
7.8 years ago by William ★ 5.3k
1
vote
1
reply
2.1k
views
Answer: A: Produce raw SNP calls
7.8 years ago by William ★ 5.3k
3
votes
1
reply
44k
views
Answer: A: How to filter vcf file on minimum genotype depth and quality for each sample
7.8 years ago by William ★ 5.3k
0
votes
1
reply
44k
views
Comment: C: How to filter vcf file on minimum genotype depth and quality for each sample
7.8 years ago by William ★ 5.3k
0
votes
1
reply
44k
views
Comment: C: How to filter vcf file on minimum genotype depth and quality for each sample
7.8 years ago by William ★ 5.3k
385 results • Page 3 of 8
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