User: siyavash_damdar
siyavash_damdar • 20
- Reputation:
- 20
- Status:
- New User
- Location:
- Last seen:
- 20 hours ago
- Joined:
- 9 months, 1 week ago
- Email:
- s**************@yahoo.com
Posts by siyavash_damdar
<prev
• 35 results •
page 1 of 4 •
next >
3
votes
2
answers
247
views
2
answers
... Hi,
I have many coordinates (approximatly1000), I want to know how can I find the gene symbols that are in these coordinates?
Thanks,
Siavash ...
written 4 months ago by
siyavash_damdar • 20
• updated
4 months ago by
Alex Reynolds ♦ 26k
0
votes
0
answers
347
views
0
answers
... Hi to all, I have a vcf file that including multisample. I want to calculate expected heterozygosity for this vcf file by sliding-window approach(40-kb-windows slidingin20-kb-steps).
I want to know, which software do this?
Thanks,
Siavash ...
written 4 months ago by
siyavash_damdar • 20
0
votes
1
answer
320
views
1
answers
... Hi
Thank you for useful comment. Yes of course, I did it.
The best,
Siavash ...
written 5 months ago by
siyavash_damdar • 20
0
votes
1
answer
320
views
1
answers
... sorry if bother you. Thanks ...
written 5 months ago by
siyavash_damdar • 20
0
votes
1
answer
320
views
1
answers
... so, according to your comments, I can have 3 scenarios:
1. call sample by sample and joint genotype
2.call all samples per region
3. call all samples (all regions) using multithreading
so, Are there any differences in the results (genotypes) of these scenarios?
...
written 5 months ago by
siyavash_damdar • 20
0
votes
1
answer
320
views
1
answers
... what are you thinking if I increase my memory an thread (RAM 64 and 16 thread)? ...
written 5 months ago by
siyavash_damdar • 20
0
votes
1
answer
320
views
1
answers
... so you mean my command is not a true way for all samples variant calling?
java -Xmx16g -jar GenomeAnalysisTK-3.8-0-ge9d806836/GenomeAnalysisTK.jar -R Equus_caballus.EquCab2.dna.toplevel.fa -T HaplotypeCaller -I sample-1.bam -I sample-2 -I sample-3 ......-I sample-60 -ERC GVCF -o output.vcf. ...
written 5 months ago by
siyavash_damdar • 20
0
votes
1
answer
320
views
1
answers
... thank you for your attention. I mean can I do variant calling for 60 samples or I should do it separately for each sample?
because when I do it separately for each sample, I have only two Genotypes per SNP (0/1 or 1/1) in g.vcf files. ...
written 5 months ago by
siyavash_damdar • 20
3
votes
1
answer
320
views
1
answer
... Hi
I want to do variant calling for more than 60 samples using haplotype caller. I want to know, I should do it with multiple samples using this command :
java -Xmx16g -jar GenomeAnalysisTK-3.8-0-ge9d806836/GenomeAnalysisTK.jar -R Equus_caballus.EquCab2.dna.toplevel.fa -T HaplotypeCaller -I s ...
written 5 months ago by
siyavash_damdar • 20
0
votes
2
answers
241
views
2
answers
Comment:
C: mapping form different lane
... I want for SNP discovery. so if I want to map all files in one step then I faced problems in GATK? is it true?
...
written 5 months ago by
siyavash_damdar • 20
Latest awards to siyavash_damdar
No awards yet. Soon to come :-)
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 1084 users visited in the last hour