4
votes
3
replies
193
views
0
votes
2
replies
137
views
updated 7 weeks ago by
brunobsouzaa
▴
540
•
written 7 weeks ago by
enes
▴
10
24
votes
0
replies
1.5k
views
9 months ago by
Malachi Griffith
19k
2
votes
2
replies
257
views
updated 16 months ago by
colindaven
★
3.0k
•
written 16 months ago by
marongiu.luigi
▴
570
0
votes
0
replies
242
views
3
votes
1
reply
2.8k
views
23 months ago by
anna
▴
10
1
vote
0
replies
1.2k
views
2.1 years ago by
Adrian
▴
10
0
votes
4
replies
1.5k
views
updated 2.7 years ago by
Biostar
20
•
written 2.7 years ago by
marongiu.luigi
▴
570
3
votes
5
replies
3.8k
views
updated 3.5 years ago by
trustedagent1
•
0
•
written 7.0 years ago by
Moses M. Feaster
▴
30
2
votes
3
replies
983
views
0
votes
2
replies
3.0k
views
2
votes
2
replies
2.1k
views
4.5 years ago by
aphatak
▴
40
2
votes
2
replies
2.2k
views
5.7 years ago by
fing
•
0
1
vote
1
reply
2.2k
views
6.1 years ago by
Na Sed
▴
310
0
votes
0
replies
1.6k
views
6.2 years ago by
dinesh
▴
50
1
vote
0
replies
2.0k
views
updated 4 months ago by
Ram
34k
•
written 6.3 years ago by
mehran.karimzade
▴
190
18
votes
5
replies
18k
views
1
vote
7
replies
2.1k
views
updated 6.4 years ago by
Istvan Albert
88k
•
written 6.4 years ago by
Affan
▴
290
2
votes
1
reply
2.4k
views
3
votes
5
replies
3.9k
views
7.0 years ago by
Moses M. Feaster
▴
30
Recent Votes
Recent Locations •
All
Spain, 5 minutes ago
United States, 9 minutes ago
Canada/University of Manitoba, 9 minutes ago
United States, 13 minutes ago
Australia, 13 minutes ago
South Korea, 17 minutes ago
United States, 19 minutes ago
Recent Awards •
All
Supporter to
etiennedanis
•
0
Rising Star to
rheab1230
•
0
Teacher to
WouterDeCoster
45k
Teacher to
Kevin Blighe
75k
Scholar to
Mensur Dlakic
★
12k
Popular Question to
irfanwustl
▴
20
Recent Replies
Comment: inquiry related to snpsift
by
Kevin Blighe
75k
Please paste the entire header of the file file_chr2.vcf
hint: `bcftools view -h file_chr2.vcf`
Comment: inquiry related to snpsift
by
rheab1230
•
0
Hi,
I use the above command
But I am getting error
the error:
[W::bcf_hdr_check_sanity] GL should be declared as Number=G
[W::vcf_…
Answer: How do I perform a plot from admixture analysis with multiple runs
by
alexis.diaz
•
0
I found the answer, you need first to move all *Q files from each K into a single folder.
Next, you should process this folder using 'pop…
Answer: Would this laptop be sufficient for small dataset/sequence analysis?
by
Kevin Blighe
75k
Just adding:
My own laptop, purchased in 2015 in London (London UK, not London Ontario), is 16GB RAM, 4-core CPU, and 2TB hard-disk. Rig…
Comment: inquiry related to snpsift
by
Kevin Blighe
75k
Hi again, have you tried to index the VCF as suggested?
Actually, you may need this sequence of commands:
bcftools annotate --remove …
Comment: How To Split A Bam File By Chromosome
by
Jorge Amigo
13k
Of course it depends on how your chromosomes are defined. If your bam file comes from a hg19 mapping you'll have to use "chr1", and if your…
Comment: SNP filtering
by
rheab1230
•
0
I didn't understand.
I am sorry but i am completely new to bioinformatics.
Should i use the following command:
tabix -p GEUVADIS.chr1.geno…
Answer: How to generate a .sam/.bam file of a particular chromosome or even a particular
by
etiennedanis
•
0
```samtools view -b in.bam chr1:100000-200000 > out.bam``` did not work for me.
But ```samtools view -b in.bam 1:100000-200000 > out.bam``…
Answer: Would this laptop be sufficient for small dataset/sequence analysis?
by
brian.fristensky
▴
220
1. I agree that 16 Gb RAM is probably not enough. **Buy as much RAM as you can afford**, even at the expense of disk space. Disk is cheap…
Comment: inquiry related to snpsift
by
rheab1230
•
0
I use the above command as mentioned by you. the commands:
bcftools annotate -x ID file_chr2.vcf
the error: [W::bcf_hdr_check_s…
Comment: inquiry related to snpsift
by
rheab1230
•
0
I actually just added one part of the input file.
8,-0.48:0.150:.:. 0|0:-0.48,-0.48,-0.48:0.200:.:. 0|0:-0.48,-0.48,-0.48:0.350:.:. 0|0:-0.…
Answer: Would this laptop be sufficient for small dataset/sequence analysis?
by
Mensur Dlakic
★
12k
16 GB of RAM will not cut it for any serious bioinformatics application these days. Doubly so if you choose to run Windows.
Comment: inquiry related to snpsift
by
Kevin Blighe
75k
I see - thanks. I am not sure that `SnpSift annotate` can do this, but you can first remove the original ID via `bcftools`, as follows:
…
Answer: Forum: Job opportunities in Europe, with and without a PhD
by
Kevin Blighe
75k
South Africa? - very nice. I had been considering moving there, would you believe.
There is no correct answer to your question, and one ca…
Comment: inquiry related to snpsift
by
rheab1230
•
0
the command:
java -jar SnpSift.jar annotate dbSnp144.vcf variants.vcf > variants_annotated.vcf
I am getting no error.
the input file …
Traffic: 984 users visited in the last hour
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by the
version 2.3.6
version 2.3.6