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Search: Posts Made By: david.tamborero
Forum: Bioinformatics 04-15-2014, 02:02 AM
Replies: 0
Views: 1,133
Posted By david.tamborero
interpret a somatic mutation labelled in dbsnp

Hi,

I am analysing somatic mutations that -theoretically- have been already filtered for SNPs -I'm not involved in the mutation pipeline-; the point is that by checking them by my own I've found...
Forum: Bioinformatics 10-04-2013, 06:46 AM
Replies: 3
Views: 2,701
Posted By david.tamborero
I mean, I notice that I can retrieve this info...

I mean, I notice that I can retrieve this info from another commands of the package, so I will do it (or using other means, as the Ensembl api) if no easier way to do that exists in some magic...
Forum: Bioinformatics 10-04-2013, 06:41 AM
Replies: 3
Views: 2,701
Posted By david.tamborero
Thanks for your answer! FYI, the package ...

Thanks for your answer!

FYI, the package -at least in my R libs installation- is in library('GenomicFeatures')

Anyway, I quickly check the command and it seems to require that I indicate the...
Forum: Bioinformatics 10-04-2013, 06:00 AM
Replies: 3
Views: 2,701
Posted By david.tamborero
Converting mRNA coordinates to chromosome coordinates

hi,

any of you know how to (easily) change mrna coordinates of a gene to chromosomal positions (or viceversa)? Something as (figures are invented): KRAS c.819A>T to chr12:25,357,800 A>T

I...
Forum: Bioinformatics 09-28-2013, 08:40 AM
Replies: 3
Views: 2,603
Posted By david.tamborero
thanks for the answer! I think that I am...

thanks for the answer!

I think that I am going to score as 'highly deleterious' those mutations in 2 last/ 2 initial bases of introns in canonical splice sites, as I am currently doing with...
Forum: Bioinformatics 09-18-2013, 06:37 AM
Replies: 3
Views: 2,603
Posted By david.tamborero
impact of mutations in splicing sites

hi,

I would like to score the impact of mutations occurring in gene regions that the variant effect predictor state as 'splice_variant'. Note that at this moment I do not want to predict whether...
Forum: Bioinformatics 01-21-2013, 12:47 PM
Replies: 6
Views: 32,836
Posted By david.tamborero
Hi, I'm far (honestly) from being an expert...

Hi,

I'm far (honestly) from being an expert in this issue, but as far as I know, if you perform the mutation call for the tumor sample and for the normal sample separately, once you have the final...
Forum: Bioinformatics 08-20-2012, 07:07 AM
Replies: 4
Views: 3,986
Posted By david.tamborero
varscan - filter out those snps close to indels

hi,

just a quick question about the somaticFilter provided by Varscan:

--indel-file File of indels for filtering nearby SNPs

What does (exactly) it mean 'nearby'? within the same read?...
Forum: Bioinformatics 07-16-2012, 06:50 AM
Replies: 35
Views: 25,225
Posted By david.tamborero
Hi! I am trying to use the false positive...

Hi!

I am trying to use the false positive filter attached as a pl script within the Varscan source code. I've noticed that first I need to run the bam-readcount script. I've just tried it and I...
Forum: Bioinformatics 06-22-2012, 01:18 PM
Replies: 16
Views: 13,133
Posted By david.tamborero
Just for your records, Varscan really had a bug...

Just for your records, Varscan really had a bug when filtering bases according to its quality. This happened regardless of the mpileup recalibration, since I inputted dummy pileup files created by...
Forum: Bioinformatics 06-22-2012, 12:47 PM
Replies: 35
Views: 25,225
Posted By david.tamborero
Sorry for my last post, I've just found the...

Sorry for my last post, I've just found the scripts for running the false positive filter in the VArscan sourceforge page.

So it's time to go home, I will feedback the performace I will get as...
Forum: Bioinformatics 06-22-2012, 07:34 AM
Replies: 35
Views: 25,225
Posted By david.tamborero
Hi! I've returned to the 'somatic mutation...

Hi!

I've returned to the 'somatic mutation detectors' world after a long time, and I am going to check the Varscan2.

I am interested in not taking into account any SNP found near an indel. This...
Forum: Bioinformatics 06-22-2012, 07:05 AM
Replies: 7
Views: 7,046
Posted By david.tamborero
I was checking this long time ago, and now I...

I was checking this long time ago, and now I don't remember it on detail. I guess mpileup filtered out those reads that could be untrustwirthy, as those with zero-mapping quality or those improperly...
Forum: Bioinformatics 06-22-2012, 07:01 AM
Replies: 20
Views: 9,571
Posted By david.tamborero
Hi! I've just landed in this post after a...

Hi!

I've just landed in this post after a long time without using somatic calling tools.

I am wondering if you solved this, I have no idea why it happened.

Anyway, I've just downloaded the...
Forum: Bioinformatics 02-02-2012, 09:46 AM
Replies: 35
Views: 25,225
Posted By david.tamborero
Thanks for your answer, dkoboldt. I've...

Thanks for your answer, dkoboldt.

I've re-sent you a mail explaining what it seems a bug in Varscan performance during the count of ref/variant bases depending on base quality (ie. the...
Forum: Bioinformatics 02-02-2012, 09:26 AM
Replies: 20
Views: 9,571
Posted By david.tamborero
I guess than before running varscan you have...

I guess than before running varscan you have converted the bam file to pileup file, right?

If so, such 'lost' reads could be explained by the samtools mpileup command. Check its arguments: the...
Forum: Bioinformatics 01-25-2012, 09:31 AM
Replies: 0
Views: 1,448
Posted By david.tamborero
Filter out reads with several variants

Hello everyone,

I am interested in filtering out those reads containing several misalignements with the reference genome, so such reads are not taken into account when looking for variants (for...
Forum: Bioinformatics 01-25-2012, 09:19 AM
Replies: 35
Views: 25,225
Posted By david.tamborero
Hi, I was playing with Varscan and I would want...

Hi, I was playing with Varscan and I would want to give you you some feedback in case it helps:





Yes, I would say that about the Ho. On the other hand, the cut-off value for definining the...
Forum: Bioinformatics 01-23-2012, 01:56 AM
Replies: 20
Views: 9,571
Posted By david.tamborero
No idea, I only have used the somatic command....

No idea, I only have used the somatic command. You can try the other Varscan commands (as the pileup2snp) with a dummy pileup file and play with the --min-avg-qual parameter to check it out.

By...
Forum: Bioinformatics 01-22-2012, 01:12 PM
Replies: 7
Views: 7,046
Posted By david.tamborero
Just for those than can be interested in this...

Just for those than can be interested in this thread, I've found that all the reads of this sample have been accounted as anomalous reads by mpileup, so they are excluded (and thus, an empty output...
Forum: Bioinformatics 01-22-2012, 12:58 PM
Replies: 20
Views: 9,571
Posted By david.tamborero
Just for those that can be interested in the...

Just for those that can be interested in the varscan filtering according to the base quality: apparently Varscan has a bug that arises when certain characters appear in the field containing the bases...
Forum: Bioinformatics 01-14-2012, 07:51 AM
Replies: 14
Views: 4,089
Posted By david.tamborero
ok, I will download the last version to simplify...

ok, I will download the last version to simplify the interleave step.

Many thanks for your help, Nils.
Forum: Bioinformatics 01-14-2012, 07:43 AM
Replies: 14
Views: 4,089
Posted By david.tamborero
Yes, you're right. Last question: when...

Yes, you're right.
Last question: when interleaving, the second end must be reversed and complemented?

I am trying to figure out whether bfast requires all the pairs to be listed in order of 5'...
Forum: Bioinformatics 01-14-2012, 07:12 AM
Replies: 14
Views: 4,089
Posted By david.tamborero
Nils, sorry for that, but I would say that the...

Nils, sorry for that, but I would say that the reads name are the same. In the first example, they are 'illumina-like'. In the second example, they are 'fastq-like'.

So my guess is that in the...
Forum: Bioinformatics 01-11-2012, 02:28 AM
Replies: 14
Views: 4,089
Posted By david.tamborero
Hi, I have actually the same problem. I have...

Hi,

I have actually the same problem. I have each pair end of the reads in separate files, but when they look as the following:

--- pair_1 file:

@HWUSI-EAS1692_0001:1:1:1050:4451#0/1...
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