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Search: Posts Made By: mimi_lupton
Forum: Bioinformatics 09-09-2013, 10:30 PM
Replies: 1
Views: 1,911
Posted By mimi_lupton
GATK filter on FORMAT FT tag added by Variant Filtration

I am trying to filter a VCF file that has been annotated by GATK variant filtration at the sample level.
For example in variant filteration if I used;
--genotypeFilterExpression "DP <= 4"...
Forum: Bioinformatics 07-29-2013, 05:27 PM
Replies: 0
Views: 1,429
Posted By mimi_lupton
SKAT error when including covariates

:confused:I am using the SKAT program in R to try and analyse a small subset of data for just one gene looking at certain rare variants.
I run into an error when I try and add covariates into the...
Forum: Bioinformatics 07-15-2013, 03:26 PM
Replies: 7
Views: 2,177
Posted By mimi_lupton
Hi Paul, to separate out individuals from...

Hi Paul,

to separate out individuals from you VCF you can use VCFtools

http://vcftools.sourceforge.net/docs.html#filter

Annovar is good for annotation;
...
Forum: Bioinformatics 07-09-2013, 03:22 PM
Replies: 7
Views: 2,177
Posted By mimi_lupton
Hi Paul, If I understand correctly you are...

Hi Paul,
If I understand correctly you are trying to call SNPs from 96 bam files, but get one vcf file with only one individual?
You should be calling all your BAM files together to get one VCF,...
Forum: Bioinformatics 05-22-2013, 04:47 PM
Replies: 7
Views: 2,177
Posted By mimi_lupton
:DThanks for your help! Yes I needed; ...

:DThanks for your help! Yes I needed;

-D:dbsnp,vcf dbsnp_132.b37.vcf
Forum: Bioinformatics 05-21-2013, 11:56 PM
Replies: 11
Views: 2,815
Posted By mimi_lupton
I use Picard tools CalculateHsMetrics. This...

I use Picard tools CalculateHsMetrics.
This allows you to use a bed files with the target intervals, and the capture bait positions to get capture efficiency and coverage metrics on your targeted...
Forum: Bioinformatics 05-21-2013, 08:09 PM
Replies: 7
Views: 2,177
Posted By mimi_lupton
GATK UnifiedGenotyper with reducebam error

I am using GATK UnifiedGenotyper on multiple bam files for target enrichment sequencing. I get an error which although is a "user error", I can't seem to work it out! Any help would be greatly...
Forum: Literature Watch 07-13-2011, 08:15 AM
Replies: 46
Views: 38,463
Posted By mimi_lupton
Dear all, I have a couple of questions...

Dear all,
I have a couple of questions regarding CNV-seq.
I am having a play around with some DNA sequencing that is from custom capture. I have analysed some BAM files using the program. Some work...
Forum: Sample Prep / Library Generation 05-25-2011, 07:10 AM
Replies: 1
Views: 10,388
Posted By mimi_lupton
Illumina Pair end primers and adaptors for multiplexing

I would really appreciate any help with being able to decipher the different primers and adaptors in the illumina library preparation kits.


I am doing multiplex sequencing and need the Illumina...
Forum: Bioinformatics 03-03-2011, 03:24 AM
Replies: 8
Views: 6,764
Posted By mimi_lupton
Hi Laura, Thanks very much for you quick reply,...

Hi Laura,
Thanks very much for you quick reply, I have version 0.2.1 so I will download a newer one and try that.
Forum: Bioinformatics 03-03-2011, 02:49 AM
Replies: 8
Views: 6,764
Posted By mimi_lupton
Question Hi, I have a quick question about using tabix...

Hi,
I have a quick question about using tabix on the 1000 genomes data. I have used it to download some regions I am interested in. But I haven't got the header so I can't see the sample order. I...
Forum: Bioinformatics 01-17-2011, 08:10 AM
Replies: 28
Views: 16,253
Posted By mimi_lupton
Hi, I was just wondering if you got to the...

Hi,

I was just wondering if you got to the bottom of the error below. I have the exact same problem. I am working on some very low depth whole genome data, I'm not sure if it could be because the...
Forum: Bioinformatics 12-22-2010, 04:19 AM
Replies: 6
Views: 3,215
Posted By mimi_lupton
Dear all, Thanks for the posts above, that was...

Dear all,
Thanks for the posts above, that was exactly my question. I also have a additional question. I am trying to do remove duplicates with PICARD. I get an error because my input file has...
Forum: Illumina/Solexa 09-01-2010, 01:12 AM
Replies: 20
Views: 6,679
Posted By mimi_lupton
I am doing some sequencing to look at copy number...

I am doing some sequencing to look at copy number variants at low depth. Can I ask why in your paper you use 200bp fragment size, did you use paired end reads? Would it have been possible to have a...
Forum: Sample Prep / Library Generation 08-31-2010, 06:29 AM
Replies: 0
Views: 3,890
Posted By mimi_lupton
Question Insert size for paired end sequencing for identification of structural variation

Dear all,
Does anyone have any experience of the ideal fragment size for paired end sequencing looking at structural variation in whole genome sequencing?

I am doing a pilot project to whole...
Forum: Illumina/Solexa 02-08-2009, 10:41 AM
Replies: 3
Views: 2,312
Posted By mimi_lupton
Thanks for your reply, that makes thing clearer. ...

Thanks for your reply, that makes thing clearer.
Because I am looking at pools of lots of individuals I am not using the MAQ SNP calling algorithm, but calling my own SNPs using the pile up...
Forum: Illumina/Solexa 02-07-2009, 09:33 AM
Replies: 3
Views: 2,312
Posted By mimi_lupton
use of export/sequence data

Dear all,
I am analysing sequencing data for pooled samples for a candidate gene to look for rare variants. Using the data from the illumina pipeline I first used the s_N_sequence.txt filtered data...
Forum: Bioinformatics 10-31-2008, 08:48 AM
Replies: 0
Views: 1,732
Posted By mimi_lupton
Maq SNP calls from a large pool

Hi there,
I am carrying out a candidate gene re-sequencing project where I have run PCR products from a large pool of individuals (311 people) on Solexa. This means I have a very high depth of...
Forum: Introductions 10-30-2008, 09:54 AM
Replies: 0
Views: 1,704
Posted By mimi_lupton
Hi from London

Hi,
I'm Michelle Lupton, I am a PhD student at the Institute of Pyschiatry, Kings College London, currently carrying out re-sequencing of a candidate gene using pooled DNA on solexa.
I'm very...
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