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0
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0
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100
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Is there a array-based population dataset with phenotypes like eye colour available?
gwas
17 days ago by optimistsso4co3 ▴ 100
2
votes
1
reply
260
views
fastQC - how to know if sample is good quality ?
fastqc
updated 23 days ago by 38k • written 23 days ago by ▴ 100
0
votes
0
replies
217
views
Protocol to detect chromosomal ploidy from WGS VCF?
wgs ploidy
7 weeks ago by optimistsso4co3 ▴ 100
0
votes
2
replies
298
views
Can you apply Base Score Recalibration in parallel?
wgs
updated 7 weeks ago by 2.2k • written 7 weeks ago by ▴ 100
0
votes
3
replies
412
views
How to interpret deletion the length of chromosome?
del
updated 10 weeks ago by 153k • written 10 weeks ago by ▴ 100
0
votes
7
replies
642
views
Is it possible to query column of particular sample on VCF?
vcf
7 months ago by optimistsso4co3 ▴ 100
3
votes
6
replies
622
views
How to filter VCF for only variants present in particular sample?
vcf
7 months ago by optimistsso4co3 ▴ 100
1
vote
2
replies
363
views
Is it possible to annotate each person individually with VEP?
VEP
updated 8 months ago by 2.2k • written 8 months ago by ▴ 100
1
vote
1
reply
275
views
Is there a tool to standartise ANY kind of human variant list file? (like vcf, plink, 23andMe etc)
23andme
updated 8 months ago by 2.6k • written 8 months ago by ▴ 100
0
votes
1
reply
335
views
Where to find Structural variant database dgvMerged for ANNOVAR?
annovar
8 months ago by optimistsso4co3 ▴ 100
0
votes
0
replies
268
views
How to control number of cores GATK can use?
gatk
9 months ago by optimistsso4co3 ▴ 100
0
votes
0
replies
287
views
Do you have to select "pulled" or "final" bam in MELT mobile element discovery step of genotyping?
melt
9 months ago by optimistsso4co3 ▴ 100
0
votes
2
replies
407
views
Mobile element discovery with MELT brings different results when chromosomes are analysed separate
melt
9 months ago by optimistsso4co3 ▴ 100
1
vote
1
reply
308
views
Is it possible to add variant type "VT" to each variant in vcf?
bcftools
updated 10 months ago by 38k • written 10 months ago by ▴ 100
0
votes
3
replies
358
views
gatk requests enormous amounts of memory. How to limit it?
gatk
updated 10 months ago by ▴ 810 • written 10 months ago by ▴ 100
0
votes
0
replies
252
views
How to extract region from GVCF file?
GVCF
11 months ago by optimistsso4co3 ▴ 100
1
vote
1
reply
245
views
How to calculate indels per individual?
vcf
updated 13 months ago by 153k • written 13 months ago by ▴ 100
1
vote
1
reply
603
views
How to prepare vcf for use with Picard?
picard
updated 14 months ago by 153k • written 14 months ago by ▴ 100
0
votes
0
replies
276
views
How to fill vcf ALT field for sites where it's missing?
vcf
14 months ago by optimistsso4co3 ▴ 100
2
votes
2
replies
434
views
How to correct for allele frequency mismatches?
plink
14 months ago by optimistsso4co3 ▴ 100
6
votes
10
replies
997
views
Why isn't it a common practice to call variant for every position in human genome?
ngs
updated 15 months ago by 21k • written 15 months ago by ▴ 100
0
votes
1
reply
401
views
Fastest pipeline for large scale joint genotype calling?
calling
updated 15 months ago by 153k • written 15 months ago by ▴ 100
0
votes
0
replies
279
views
Is there such thing as GVCF for structural variants allowing population genetics on SVs?
sv
16 months ago by optimistsso4co3 ▴ 100
2
votes
1
reply
353
views
How to extract specific location in .bam files
bam
updated 16 months ago by 127k • written 16 months ago by ▴ 100
0
votes
1
reply
452
views
Is it correct to merge multiple gvcf from separate variant calling?
gatk
updated 16 months ago by 21k • written 16 months ago by ▴ 100
0
votes
1
reply
527
views
Wha does combineGVCFs does to loci with variant only in gVCF from another analysis?
gatk
16 months ago by optimistsso4co3 ▴ 100
0
votes
5
replies
835
views
What are "must have" data types one should extract from WGS .fq data?
wgs
updated 16 months ago by 153k • written 16 months ago by ▴ 100
6
votes
3
replies
574
views
Is it ok to replace missing WGS calls with reference notation "0/0"?
wgs
updated 16 months ago by 153k • written 16 months ago by ▴ 100
5
votes
1
reply
2.0k
views
Can someone explain PLINK allele REF/ALT management strategy?
plink
updated 17 months ago by 10.0k • written 17 months ago by ▴ 100
2
votes
1
reply
504
views
What is the largest freely available dataset of WGS samples?
wgs
updated 17 months ago by ▴ 240 • written 17 months ago by ▴ 100
0
votes
1
reply
763
views
How to best predict effect for each variant and count specific effect found in each individual using variant effect predictor?
vcf vep
updated 18 months ago by 23k • written 18 months ago by ▴ 100
2
votes
5
replies
1.3k
views
How to pass custom software specific variables to nf-core/sarek nextflow pipeline?
wgs
updated 18 months ago by ★ 1.1k • written 20 months ago by ▴ 100
4
votes
5
replies
824
views
How to paralle trim_galore for single sample?
trim_galore
updated 20 months ago by 70k • written 20 months ago by ▴ 100
0
votes
0
replies
392
views
What causes highly inflated p values of X chromosome in PLINK association analysis?
plink
2.3 years ago by optimistsso4co3 ▴ 100
0
votes
1
reply
705
views
Whats the format for PLINK .set file for epistasis analysis?
plink epistasis .set
updated 2.5 years ago by 10.0k • written 2.5 years ago by ▴ 100
0
votes
2
replies
559
views
What's the probability of genotype error at the end of 10 repeated A variants? Given low coverage sequencing of 1000G phase 1
sequencing error
2.8 years ago by optimistsso4co3 ▴ 100
0
votes
1
reply
571
views
How to save SNPs removed by quality control? Plink
plink
3.0 years ago by optimistsso4co3 ▴ 100
3
votes
3
replies
1.3k
views
Whats the point of genotype pruning before imputation?
imputation plink --indep-pariwise r2
3.7 years ago by optimistsso4co3 ▴ 100
38 results • Page 1 of 1
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