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0
votes
0
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63
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How to fill vcf ALT field for sites where it's missing?
vcf
7 days ago by optimistsso4co3 ▴ 80
2
votes
2
replies
145
views
How to correct for allele frequency mismatches?
plink
7 days ago by optimistsso4co3 ▴ 80
6
votes
10
replies
560
views
Why isn't it a common practice to call variant for every position in human genome?
ngs
updated 5 weeks ago by 20k • written 5 weeks ago by ▴ 80
0
votes
1
reply
161
views
Fastest pipeline for large scale joint genotype calling?
calling
updated 7 weeks ago by 141k • written 7 weeks ago by ▴ 80
0
votes
0
replies
98
views
Is there such thing as GVCF for structural variants allowing population genetics on SVs?
sv
7 weeks ago by optimistsso4co3 ▴ 80
2
votes
1
reply
162
views
How to extract specific location in .bam files
bam
updated 7 weeks ago by 111k • written 7 weeks ago by ▴ 80
0
votes
1
reply
187
views
Is it correct to merge multiple gvcf from separate variant calling?
gatk
updated 9 weeks ago by 20k • written 9 weeks ago by ▴ 80
0
votes
1
reply
280
views
Wha does combineGVCFs does to loci with variant only in gVCF from another analysis?
gatk
10 weeks ago by optimistsso4co3 ▴ 80
0
votes
5
replies
432
views
What are "must have" data types one should extract from WGS .fq data?
wgs
updated 11 weeks ago by 141k • written 11 weeks ago by ▴ 80
6
votes
3
replies
267
views
Is it ok to replace missing WGS calls with reference notation "0/0"?
wgs
updated 11 weeks ago by 141k • written 11 weeks ago by ▴ 80
4
votes
1
reply
370
views
Can someone explain PLINK allele REF/ALT management strategy?
plink
updated 11 weeks ago by 8.8k • written 11 weeks ago by ▴ 80
2
votes
1
reply
290
views
What is the largest freely available dataset of WGS samples?
wgs
updated 12 weeks ago by ▴ 170 • written 12 weeks ago by ▴ 80
0
votes
1
reply
487
views
How to best predict effect for each variant and count specific effect found in each individual using variant effect predictor?
vcf vep
updated 3 months ago by 23k • written 3 months ago by ▴ 80
1
vote
5
replies
754
views
How to pass custom software specific variables to nf-core/sarek nextflow pipeline?
wgs
updated 4 months ago by ▴ 800 • written 6 months ago by ▴ 80
4
votes
5
replies
494
views
How to paralle trim_galore for single sample?
trim_galore
updated 6 months ago by 57k • written 6 months ago by ▴ 80
0
votes
0
replies
241
views
What causes highly inflated p values of X chromosome in PLINK association analysis?
plink
14 months ago by optimistsso4co3 ▴ 80
0
votes
1
reply
454
views
Whats the format for PLINK .set file for epistasis analysis?
plink epistasis .set
updated 15 months ago by 8.8k • written 15 months ago by ▴ 80
0
votes
2
replies
322
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
20 months ago by optimistsso4co3 ▴ 80
0
votes
1
reply
374
views
How to save SNPs removed by quality control? Plink
plink
22 months ago by optimistsso4co3 ▴ 80
3
votes
3
replies
989
views
Whats the point of genotype pruning before imputation?
imputation plink --indep-pariwise r2
2.5 years ago by optimistsso4co3 ▴ 80
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