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Showing :
questions
8
votes
15
replies
15k
views
7 follow
Iterating through paired-end reads in samtools / pysam
BAM
SAM
Python
updated 2.8 years ago by
litun
• 0 • written 6.8 years ago by
olavur
▴ 150
10
votes
3
replies
6.5k
views
How to add trio information to VCF or PED format (to compute Mendel error in Plink)
plink
vcftools
SNP
updated 5.8 years ago by
Biostar
20 • written 7.9 years ago by
olavur
▴ 150
3
votes
14
replies
5.8k
views
Is there a tool or method for phasing a VCF based on an already phased BAM?
vcf
bam
phasing
haplotype
6.2 years ago by
olavur
▴ 150
3
votes
3
replies
2.0k
views
Variants with multiple functional annotations -- counting occurrences
VCF
annotation
updated 6.9 years ago by
Kevin Blighe
88k • written 6.9 years ago by
olavur
▴ 150
7
votes
2
replies
5.7k
views
Call missing variants in VCF as reference allele
SNP
genome
VCF
7.3 years ago by
olavur
▴ 150
7
votes
13
replies
11k
views
Samtools gives "truncated file" when trying to view a "reheaded" file
software error
next-gen
sequence
samtools
updated 7.4 years ago by
Devon Ryan
105k • written 7.4 years ago by
olavur
▴ 150
4
votes
11
replies
4.8k
views
NGS data storage and management
next-gen
NGS
databases
genome browsers
updated 6 months ago by
menyawino
• 0 • written 7.4 years ago by
olavur
▴ 150
7
votes
10
replies
3.9k
views
How can I create a dummy dataset from my NGS whole-exome data?
next-gen
FASTQ
alignment
updated 2.3 years ago by
rbj
▴ 40 • written 7.5 years ago by
olavur
▴ 150
7
votes
6
replies
3.4k
views
When should you de novo assemble a whole-genome, and when should you simply align it to a reference?
assembly
alignment
whole-genome
updated 7.6 years ago by
Istvan Albert
102k • written 7.6 years ago by
olavur
▴ 150
4
votes
2
replies
2.3k
views
What is contained in the GRCh38 reference, and how was it constructed?
genome
Assembly
next-gen
updated 7.6 years ago by
Istvan Albert
102k • written 7.6 years ago by
olavur
▴ 150
0
votes
2
replies
3.0k
views
Full-stop/period as SNP identifier in BIM file causes error in Plink v1.9 --read-freq command
plink
snp
updated 7.7 years ago by
sbk
▴ 60 • written 7.7 years ago by
olavur
▴ 150
4
votes
10
replies
4.1k
views
Inconsistency in VCF and Plink format after conversion
vcftools
plink
7.8 years ago by
olavur
▴ 150
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