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8
votes
15
replies
13k
views
7 follow
Iterating through paired-end reads in samtools / pysam
BAM
SAM
Python
updated 2.5 years ago by
litun
• 0 • written 6.4 years ago by
olavur
▴ 150
10
votes
3
replies
6.3k
views
How to add trio information to VCF or PED format (to compute Mendel error in Plink)
plink
vcftools
SNP
updated 5.4 years ago by
Biostar
20 • written 7.5 years ago by
olavur
▴ 150
0
votes
0
replies
5.4k
views
Comment:
C: Is there a tool or method for phasing a VCF based on an already phased BAM?
5.6 years ago by
olavur
▴ 150
0
votes
2
replies
5.4k
views
Comment:
C: Is there a tool or method for phasing a VCF based on an already phased BAM?
5.6 years ago by
olavur
▴ 150
0
votes
0
replies
5.4k
views
Comment:
C: Is there a tool or method for phasing a VCF based on an already phased BAM?
5.6 years ago by
olavur
▴ 150
3
votes
14
replies
5.4k
views
Is there a tool or method for phasing a VCF based on an already phased BAM?
vcf
bam
phasing
haplotype
5.8 years ago by
olavur
▴ 150
0
votes
1
reply
5.4k
views
Comment:
C: Is there a tool or method for phasing a VCF based on an already phased BAM?
5.8 years ago by
olavur
▴ 150
0
votes
0
replies
5.4k
views
Comment:
C: Is there a tool or method for phasing a VCF based on an already phased BAM?
5.8 years ago by
olavur
▴ 150
0
votes
1
reply
5.4k
views
Comment:
C: Is there a tool or method for phasing a VCF based on an already phased BAM?
5.8 years ago by
olavur
▴ 150
0
votes
1
reply
5.4k
views
Comment:
C: Is there a tool or method for phasing a VCF based on an already phased BAM?
5.8 years ago by
olavur
▴ 150
0
votes
1
reply
13k
views
Comment:
C: Iterating through paired-end reads in samtools / pysam
6.0 years ago by
olavur
▴ 150
0
votes
0
replies
13k
views
Comment:
C: Iterating through paired-end reads in samtools / pysam
6.1 years ago by
olavur
▴ 150
0
votes
0
replies
13k
views
Comment:
C: Iterating through paired-end reads in samtools / pysam
6.4 years ago by
olavur
▴ 150
0
votes
1
reply
13k
views
Comment:
C: Iterating through paired-end reads in samtools / pysam
6.4 years ago by
olavur
▴ 150
0
votes
1
reply
1.9k
views
Comment:
C: Variants with multiple functional annotations -- counting occurrences
6.5 years ago by
olavur
▴ 150
3
votes
3
replies
1.9k
views
Variants with multiple functional annotations -- counting occurrences
VCF
annotation
updated 6.5 years ago by
Kevin Blighe
88k • written 6.5 years ago by
olavur
▴ 150
0
votes
0
replies
3.7k
views
Comment:
C: vcf-merge is giving me a few SNPs in the merged vcf file
6.7 years ago by
olavur
▴ 150
0
votes
0
replies
3.7k
views
Answer:
A: vcf-merge is giving me a few SNPs in the merged vcf file
6.7 years ago by
olavur
▴ 150
1
vote
0
replies
5.6k
views
Comment:
C: Call missing variants in VCF as reference allele
6.9 years ago by
olavur
▴ 150
7
votes
2
replies
5.6k
views
Call missing variants in VCF as reference allele
SNP
genome
VCF
6.9 years ago by
olavur
▴ 150
0
votes
1
reply
10k
views
Comment:
C: Samtools gives "truncated file" when trying to view a "reheaded" file
7.0 years ago by
olavur
▴ 150
0
votes
1
reply
10k
views
Comment:
C: Samtools gives "truncated file" when trying to view a "reheaded" file
7.0 years ago by
olavur
▴ 150
0
votes
2
replies
10k
views
Comment:
C: Samtools gives "truncated file" when trying to view a "reheaded" file
7.0 years ago by
olavur
▴ 150
7
votes
13
replies
10k
views
Samtools gives "truncated file" when trying to view a "reheaded" file
software error
next-gen
sequence
samtools
updated 7.0 years ago by
Devon Ryan
104k • written 7.0 years ago by
olavur
▴ 150
0
votes
1
reply
4.5k
views
Comment:
C: NGS data storage and management
7.0 years ago by
olavur
▴ 150
0
votes
0
replies
4.5k
views
Comment:
C: NGS data storage and management
7.0 years ago by
olavur
▴ 150
0
votes
0
replies
2.0k
views
Comment:
C: GaTK reverse select interval list
7.0 years ago by
olavur
▴ 150
0
votes
0
replies
4.5k
views
Comment:
C: NGS data storage and management
7.0 years ago by
olavur
▴ 150
0
votes
0
replies
4.5k
views
Comment:
C: NGS data storage and management
7.0 years ago by
olavur
▴ 150
4
votes
11
replies
4.5k
views
NGS data storage and management
next-gen
NGS
databases
genome browsers
updated 7 weeks ago by
menyawino
• 0 • written 7.0 years ago by
olavur
▴ 150
0
votes
1
reply
4.5k
views
Comment:
C: NGS data browser and
7.0 years ago by
olavur
▴ 150
0
votes
0
replies
3.7k
views
Comment:
C: How can I create a dummy dataset from my NGS whole-exome data?
7.1 years ago by
olavur
▴ 150
0
votes
2
replies
3.7k
views
Comment:
C: How can I create a dummy dataset from my NGS whole-exome data?
7.1 years ago by
olavur
▴ 150
0
votes
1
reply
3.7k
views
Comment:
C: How can I create a dummy dataset from my NGS whole-exome data?
7.1 years ago by
olavur
▴ 150
7
votes
10
replies
3.7k
views
How can I create a dummy dataset from my NGS whole-exome data?
next-gen
FASTQ
alignment
updated 22 months ago by
rbj
▴ 40 • written 7.1 years ago by
olavur
▴ 150
0
votes
1
reply
3.2k
views
Comment:
C: When should you de novo assemble a whole-genome, and when should you simply alig
7.2 years ago by
olavur
▴ 150
0
votes
1
reply
3.2k
views
Comment:
C: When should you de novo assemble a whole-genome, and when should you simply alig
7.2 years ago by
olavur
▴ 150
7
votes
6
replies
3.2k
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 7.2 years ago by
Istvan Albert
101k • written 7.2 years ago by
olavur
▴ 150
4
votes
2
replies
2.2k
views
What is contained in the GRCh38 reference, and how was it constructed?
genome
Assembly
next-gen
updated 7.2 years ago by
Istvan Albert
101k • written 7.2 years ago by
olavur
▴ 150
0
votes
2
replies
2.9k
views
Full-stop/period as SNP identifier in BIM file causes error in Plink v1.9 --read-freq command
plink
snp
updated 7.3 years ago by
sbk
▴ 60 • written 7.3 years ago by
olavur
▴ 150
0
votes
0
replies
3.9k
views
Comment:
C: Inconsistency in VCF and Plink format after conversion
7.4 years ago by
olavur
▴ 150
1
vote
1
reply
3.9k
views
Comment:
C: problem with vcf file
7.4 years ago by
olavur
▴ 150
0
votes
0
replies
3.9k
views
Comment:
C: Inconsistency in VCF and Plink format after conversion
7.4 years ago by
olavur
▴ 150
0
votes
1
reply
3.9k
views
Comment:
C: Inconsistency in VCF and Plink format after conversion
7.4 years ago by
olavur
▴ 150
4
votes
10
replies
3.9k
views
Inconsistency in VCF and Plink format after conversion
vcftools
plink
7.4 years ago by
olavur
▴ 150
0
votes
1
reply
3.9k
views
Comment:
C: Inconsistency in VCF and Plink format after conversion
7.4 years ago by
olavur
▴ 150
0
votes
1
reply
3.9k
views
Comment:
C: Inconsistency in VCF and Plink format after conversion
7.4 years ago by
olavur
▴ 150
3
votes
0
replies
6.3k
views
Answer:
A: How to add trio information to VCF or PED format (to compute Mendel error in Pli
7.5 years ago by
olavur
▴ 150
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