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Forum: Bioinformatics 03-19-2012, 07:50 AM
Replies: 14
Views: 9,187
Posted By raonyguimaraes
Can you post the first 20 lines of your VCF file...

Can you post the first 20 lines of your VCF file ?

results/1000G_omni2.5.hg19.sites.vcf

results/hapmap_3.3.hg19.vcf
Forum: Bioinformatics 12-22-2011, 05:57 PM
Replies: 3
Views: 7,665
Posted By raonyguimaraes
http://biostar.stackexchange.com/questions/771/con...

http://biostar.stackexchange.com/questions/771/converting-bam-to-fastq

:)
Forum: Bioinformatics 12-13-2011, 03:37 PM
Replies: 1
Views: 2,748
Posted By raonyguimaraes
1000Genomes YRI trio, NCBI36/37, rs334

Hello all!

I was asked to download the data of a trio of YRI from the 1000genomes Project. So I looked at all the data published by the project and I found a release with the file above that had...
Forum: Bioinformatics 11-16-2011, 04:41 PM
Replies: 3
Views: 7,960
Posted By raonyguimaraes
Thanks a lot Carlos, I was planning to do...

Thanks a lot Carlos, I was planning to do something similar with this thread http://seqanswers.com/forums/showthread.php?t=14038

Now I can use your workflow to start !

For dbSNP ROD I usually...
Forum: General 11-15-2011, 05:23 AM
Replies: 5
Views: 4,661
Posted By raonyguimaraes
http://i.imgur.com/LRn0Yl.gif

http://i.imgur.com/LRn0Yl.gif
Forum: Bioinformatics 11-04-2011, 02:13 AM
Replies: 12
Views: 6,443
Posted By raonyguimaraes
No it shoudln't take that long ... but this is...

No it shoudln't take that long ... but this is proportional to your computer's capabilities ... What is your config (specially processors)? Are you using threads in GATK ? How many ? :)
Forum: Bioinformatics 10-29-2011, 06:42 AM
Replies: 7
Views: 5,426
Posted By raonyguimaraes
First of all, extract metrics from your Alignment...

First of all, extract metrics from your Alignment to check if they are ok, if they are may be it's because you are using a very high coverage 5000 means 500X of coverage ... Are you sure you have...
Forum: Bioinformatics 10-27-2011, 09:41 AM
Replies: 7
Views: 5,426
Posted By raonyguimaraes
May be there is something wrong with the score of...

May be there is something wrong with the score of your FASTQ files. Are you using Illumina or Phred Scores ? You could try to use BWA for the alignment.
Forum: Bioinformatics 10-27-2011, 08:56 AM
Replies: 138
Views: 70,102
Posted By raonyguimaraes
dad

Hello all, I have good news ...

After using annovar, I finally got to the number of 22709 variants on my data.

From there I'm now trying to filter based on this approach:...
Forum: Bioinformatics 10-26-2011, 04:22 PM
Replies: 138
Views: 70,102
Posted By raonyguimaraes
I rerunned all my analysis several times since...

I rerunned all my analysis several times since the alignment using BWA -I option till UnifiedGenotyper and I'm still getting this output from UnifiedGenotyper:

Visited bases ...
Forum: Bioinformatics 10-26-2011, 07:29 AM
Replies: 138
Views: 70,102
Posted By raonyguimaraes
Please use everything from resource bundle ......

Please use everything from resource bundle ... http://www.broadinstitute.org/gsa/wiki/index.php/GATK_resource_bundle
Forum: Bioinformatics 10-25-2011, 05:00 PM
Replies: 138
Views: 70,102
Posted By raonyguimaraes
If I'm not wrong ucsc.hg19.dict should be on the...

If I'm not wrong ucsc.hg19.dict should be on the same directory of the reference file.
Forum: Bioinformatics 10-25-2011, 09:39 AM
Replies: 138
Views: 70,102
Posted By raonyguimaraes
Post your command line here... and the full error...

Post your command line here... and the full error message
Forum: Bioinformatics 10-18-2011, 04:07 AM
Replies: 138
Views: 70,102
Posted By raonyguimaraes
Smile Did you try with -B:targetIntervals,BED...

Did you try with -B:targetIntervals,BED hg18_exonIntervals.bed? :)

By the way I couldn't figure out how to use this on version 1.2
Forum: Bioinformatics 10-13-2011, 05:43 PM
Replies: 138
Views: 70,102
Posted By raonyguimaraes
I think we should all give a try to VAAST as well...

I think we should all give a try to VAAST as well :)

http://www.yandell-lab.org/software/vaast.html

A probabilistic disease-gene finder for personal genomes....
Forum: Bioinformatics 10-11-2011, 06:55 AM
Replies: 138
Views: 70,102
Posted By raonyguimaraes
You are right, without using this bed file I was...

You are right, without using this bed file I was getting something like 2 million variants ... ;)
Forum: Bioinformatics 10-11-2011, 06:52 AM
Replies: 138
Views: 70,102
Posted By raonyguimaraes
On the Unifier Genotyper I'm using the following...

On the Unifier Genotyper I'm using the following parameters:

# # #Standard Raw VCF
java -Xmx15g -jar $GATK_DIR/GenomeAnalysisTK.jar -T UnifiedGenotyper \
-l INFO \
-I...
Forum: Bioinformatics 10-11-2011, 06:30 AM
Replies: 138
Views: 70,102
Posted By raonyguimaraes
All right, Here is my pipeline, some metrics...

All right,

Here is my pipeline, some metrics and logs ...

Even after using a bed file from "SeqCap EZ Human Exome Library v2.0" i'm still getting 350191 variants ... Hope someone can help me to...
Forum: Bioinformatics 10-10-2011, 07:08 PM
Replies: 2
Views: 4,983
Posted By raonyguimaraes
Probably all the files you will need are avaiable...

Probably all the files you will need are avaiable at :

ftp://ftp.broadinstitute.org/bundle/1.2/hg19/

For indels you should use the file:...
Forum: Events / Conferences 10-10-2011, 07:02 PM
Replies: 3
Views: 2,047
Posted By raonyguimaraes
You know, they could think more about how to...

You know, they could think more about how to transmit this events online using Ustream or Justin.tv ...

Or at least release the recorded sessions after the congress somewhere like in Seqanswers ?...
Forum: Bioinformatics 10-10-2011, 06:37 PM
Replies: 138
Views: 70,102
Posted By raonyguimaraes
One question. How many raw snps you are getting...

One question. How many raw snps you are getting after running Unifier Genotyper for the first time ?

Here I'm getting about 300 000 snps and I think there is something wrong with this numbers ......
Forum: Bioinformatics 10-10-2011, 06:25 PM
Replies: 138
Views: 70,102
Posted By raonyguimaraes
Thank you so much for posting this pipeline, I've...

Thank you so much for posting this pipeline, I've been doing the same for some time. Tomorrow I will post some comments about my results so far.

I think you could sum this pipeline to yours:
...
Forum: Bioinformatics 09-07-2011, 05:56 AM
Replies: 7
Views: 3,801
Posted By raonyguimaraes
So I guess we are trying to do the same analysis...

So I guess we are trying to do the same analysis :)

I think, you don't need rod files anymore, you should use VCF files instead

To calculate the depth of coverage:
...
Forum: Bioinformatics 09-07-2011, 05:34 AM
Replies: 7
Views: 3,801
Posted By raonyguimaraes
Yes I know where you can get, the problem is that...

Yes I know where you can get, the problem is that it's not public yet :)

https://svn.broadinstitute.org/Sting/branches/expIndelInUG/python/genomicAnnotatorScripts/GenerateTranscriptToInfo.py
Forum: Bioinformatics 09-07-2011, 05:25 AM
Replies: 12
Views: 9,952
Posted By raonyguimaraes
The best tip i can give you is to use the data...

The best tip i can give you is to use the data from Broad in your analysis.


ftp://ftp.broadinstitute.org/pub/seq/references/Homo_sapiens_assembly19.fasta
And...
Showing results 1 to 25 of 38

 


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