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Comment: Comment: keep samples that carry non-reference allele in list of variants snpeff/snpsift
2.9 years ago by curious ▴ 820
3
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4
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1.3k
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keep samples that carry non-reference allele in list of variants snpeff/snpsift
snpeff snpsift bcftools
2.9 years ago by curious ▴ 820
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1
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869
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subset vcf to keep only samples heterozygous or homozygous for the alternate allele of a given variant
bcftools
updated 2.9 years ago by ★ 1.1k • written 2.9 years ago by ▴ 820
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1
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1.6k
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Answer: Answer: Haploview.jar
3.0 years ago by curious ▴ 820
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3.9k
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Comment: Comment: Applying Machine Learning on vcf file
3.1 years ago by curious ▴ 820
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0
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1.6k
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Answer: Answer: New datasets for ancestry estimation and imputation?
3.2 years ago by curious ▴ 820
1
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1
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884
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inner merge vcfs in one step?
bcftools
updated 3.2 years ago by 164k • written 3.2 years ago by ▴ 820
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1
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3.9k
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Comment: Comment: Applying Machine Learning on vcf file
3.2 years ago by curious ▴ 820
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0
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538
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Is it possible to report the allele frequency of integer copy numbers >= 3?
cn.mops cnv
3.3 years ago by curious ▴ 820
2
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1
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635
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how to get exon regions for this gene w/ build 19 coordinates
bed
updated 3.3 years ago by 148k • written 3.3 years ago by ▴ 820
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0
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2.5k
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Answer: Answer: Snakemake bwa mem
3.3 years ago by curious ▴ 820
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0
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1.1k
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Answer: Answer: What is the best software for "phasing" in human population genomics with trio f
3.3 years ago by curious ▴ 820
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2
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1.6k
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Comment: Comment: is local ancestry inference typically always run w/ array genotypes instead of
3.4 years ago by curious ▴ 820
1
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4
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1.6k
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is local ancestry inference typically always run w/ array genotypes instead of imputed genotypes?
ancestry
updated 3.4 years ago by 4.5k • written 3.4 years ago by ▴ 820
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0
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1.0k
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Comment: Comment: RFMix v2 - ancestry per individual marker
3.4 years ago by curious ▴ 820
2
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7
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2.8k
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How do I log into this ftp server and look around?
ftp
updated 3.4 years ago by ★ 28k • written 3.4 years ago by ▴ 820
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2.8k
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Comment: Comment: How do I log into this ftp server and look around?
3.4 years ago by curious ▴ 820
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2
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2.8k
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Comment: Comment: How do I log into this ftp server and look around?
3.4 years ago by curious ▴ 820
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0
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3.4k
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Comment: Comment: Highly used R packages with no Python equivalent
3.4 years ago by curious ▴ 820
0
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0
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548
views
is it possible to subset samples and reheader a vcf in a single step?
bcftools
3.4 years ago by curious ▴ 820
0
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0
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908
views
can you use LD scores from build 37 reference to get LD score intercept on build 38 summary stats?
ld regression score
3.4 years ago by curious ▴ 820
0
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2
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6.8k
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Comment: Comment: sorting a multi-sample (genotype) vcf file
3.5 years ago by curious ▴ 820
4
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2
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1.9k
views
You can't just liftover from one build to another using only coordinates correct?
liftover
updated 3.5 years ago by ▴ 10 • written 4.0 years ago by ▴ 820
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0
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2.3k
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Comment: Comment: what pihat cutoffs from plink --genome are 3rd degree relative
3.6 years ago by curious ▴ 820
1
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1
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2.3k
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what pihat cutoffs from plink --genome are 3rd degree relative
related ibd plink
3.6 years ago by curious ▴ 820
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1
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1.3k
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Comment: Comment: Make map file with recombination rate using plink?
3.6 years ago by curious ▴ 820
0
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3
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1.3k
views
Make map file with recombination rate using plink?
germline plink
updated 3.6 years ago by 2.9k • written 3.6 years ago by ▴ 820
0
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0
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927
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Comment: Comment: how to identify haplotypes and its frequency based SNP genotyping data?
3.6 years ago by curious ▴ 820
0
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0
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657
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Comment: Comment: Does this output indicate my bam is paired end?
3.7 years ago by curious ▴ 820
1
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2
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657
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Does this output indicate my bam is paired end?
samtools
3.7 years ago by curious ▴ 820
2
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0
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2.6k
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Answer: Answer: How to connect HLA alleles with rsID?
3.7 years ago by curious ▴ 820
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1
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1.1k
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Comment: Comment: Could someone help me check what genomic position is this variant nomenclature r
3.7 years ago by curious ▴ 820
1
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5
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1.1k
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Could someone help me check what genomic position is this variant nomenclature referring to ?
nomeclature
updated 3.7 years ago by 21k • written 3.7 years ago by ▴ 820
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0
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3.6k
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Answer: Answer: how to run linux code in python
3.7 years ago by curious ▴ 820
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0
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1.4k
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Comment: Comment: quick way to get samples that are NOT homozygous reference for a given record us
3.7 years ago by curious ▴ 820
0
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1
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1.4k
views
Comment: Comment: quick way to get samples that are NOT homozygous reference for a given record us
3.7 years ago by curious ▴ 820
0
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4
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1.4k
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quick way to get samples that are NOT homozygous reference for a given record using bcftools?
bcftools
3.7 years ago by curious ▴ 820
0
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0
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762
views
Does a smaller value of F from PLINK --het represent higher heterozygosity?
plink
3.7 years ago by curious ▴ 820
0
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0
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520
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is the absolute value of `plink2.eigenvec.var` from `plink2 --pca biallelic-var-wts approx` a measure of how much each SNP drives PCS?
plink
3.7 years ago by curious ▴ 820
0
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1
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849
views
Is there any way to access the --cores argument in a snakemake workflow?
snakemake
updated 2.9 years ago by ▴ 190 • written 3.8 years ago by ▴ 820
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0
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1.0k
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Comment: C: STAR alignment loop segmentation fualt (core dumped)
3.8 years ago by curious ▴ 820
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0
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1.4k
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Comment: C: How do I organize snakemake when not all jobs successfully output files from pre
3.8 years ago by curious ▴ 820
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0
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853
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Answer: A: Hardy-Weinberg equilibrium and GWAS in a livestock species (advice)
3.8 years ago by curious ▴ 820
3
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3
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1.0k
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how to use unix tools to convert VCF genotypes like '1|1' to this '2'
bcftools unix
updated 18 months ago by 44k • written 3.8 years ago by ▴ 820
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1.0k
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Comment: C: how to use unix tools to convert VCF genotypes like '1|1' to this '2'
3.8 years ago by curious ▴ 820
1
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1
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743
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"SNP" record in vcf looks like this: 6:28035427:GTA:ATA ?
vcf
3.9 years ago by curious ▴ 820
0
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0
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2.6k
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Comment: C: Merging WGS SNP array data
3.9 years ago by curious ▴ 820
0
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0
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1.3k
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Is this an OK approach for lifting over a mixture of b36 & b37 to b38 variants using rsids only?
liftover
3.9 years ago by curious ▴ 820
0
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1
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2.6k
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Comment: C: Merging WGS SNP array data
3.9 years ago by curious ▴ 820
1
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1
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2.6k
views
Comment: C: Merging WGS SNP array data
3.9 years ago by curious ▴ 820
300 results • Page 2 of 6
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