User: KJ

gravatar for KJ
KJ10
Reputation:
10
Status:
New User
Location:
Netherlands
Last seen:
1 year, 8 months ago
Joined:
3 years, 7 months ago
Email:
k**************@gmail.com

Posts by KJ

<prev • 8 results • page 1 of 1 • next >
1
vote
2
answers
2.0k
views
2
answers
Comment: C: Remove variants that are homozygous-reference (0/0) in two VCF files
... The reason for not wanting to merge are the fact that 1) bcftools merge seems to output a file that tabix can not index anymore (maybe because of the size?), and 2) the script for the next analysis step already being ready, taking single-sample VCF's as input. I ended up splitting the files by chr ...
written 3.0 years ago by KJ10
0
votes
2
answers
2.0k
views
2
answers
Comment: C: Remove variants that are homozygous-reference (0/0) in two VCF files
... Sorry for the confusion, it is indeed my intention to keep loci that are "0/1" or "1/1" in at least one sample. The above solution removes to much data. ...
written 3.0 years ago by KJ10
6
votes
2
answers
2.0k
views
2
answers
Remove variants that are homozygous-reference (0/0) in two VCF files
... Dear all, Currently I have two large VCF files that include calls that are homozygous for the reference allele. For easier analysis, I would like to remove the variants that are homozygous-ref in both VCF files (or, in *VCF-speak*, be "0/0" for both samples at the same locus). I can't be the first ...
perl sequencing next-gen awk written 3.0 years ago by KJ10 • updated 3.0 years ago by William4.4k
0
votes
1
answer
683
views
1
answers
Comment: C: Combining fastq reads of twin pairs to increase coverage
... Whole genome sequencing, yes. ...
written 3.0 years ago by KJ10
0
votes
1
answer
683
views
1
answers
Comment: C: Combining fastq reads of twin pairs to increase coverage
... I was thinking, maybe to discovere pre-twinning mutations ...
written 3.0 years ago by KJ10
0
votes
1
answer
1.2k
views
1
answers
Comment: C: Phenotype choice for one of a MZ twin pair in a genetic association study
... Yes, but preferably using both (if it's possible to correct for relatedness in your study) ...
written 3.0 years ago by KJ10
0
votes
1
answer
683
views
1
answer
Combining fastq reads of twin pairs to increase coverage
... Suppose I have fastq reads of both co-twins of monozygotic twins. Would it be beneficial to combine the fastq reads of these two people to increase coverage? Is this commonly done? I'd assume that coverage would increase hugely, with the only drawback being less sensitive to detect post-twinning mu ...
fastq next-gen twins sequencing written 3.6 years ago by KJ10 • updated 3.6 years ago by andrew.j.skelton735.7k
0
votes
1
answer
1.2k
views
1
answers
Answer: A: Phenotype choice for one of a MZ twin pair in a genetic association study
... Even though this question is a bit old, I thought I'd answer this in case anyone someone else has a question like this. Even though MZ twins are not 100% genetically identical, you can indeed assume the MZ twins to be genotypically identical when the data comes from an array. You should however nev ...
written 3.6 years ago by KJ10

Latest awards to KJ

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1465 users visited in the last hour