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Search: Posts Made By: LeonDK
Forum: Bioinformatics 08-18-2016, 05:11 AM
Replies: 2
Views: 1,885
Posted By LeonDK
Running the following on the vcf files for f in...

Running the following on the vcf files
for f in `ls -1`; do gunzip -c $f | grep -c '\.|\.'; done

Yields nothing but zeros, so it looks like you are correct.
Forum: Bioinformatics 08-18-2016, 03:19 AM
Replies: 2
Views: 1,885
Posted By LeonDK
Calculate the proportion of missing data per sample from VCF file

I have a VCFv4.2 (Sanger-imputation-service genotype data) file and I need to calculate the proportion of missing data per sample.

Each sample is encoded like so:
GT:ADS:DS:GP...
Forum: Bioinformatics 08-17-2016, 12:18 AM
Replies: 0
Views: 1,791
Posted By LeonDK
Does GWAS best-practise consensus exist?

It seems many people are using Plink and snpTest for GWAS. Is this by tradition or is does a GWAS best-practise exist?
Forum: Bioinformatics 08-16-2016, 12:09 AM
Replies: 0
Views: 1,160
Posted By LeonDK
Results of imputing single samples versus multiple (batch)

Situation 1
I have a single genotyped sample A, which I impute against HRC

Situation 2
The same sample A, is part of a batch of e.g. 500 samples, which I impute against HRC

Question
If I...
Forum: Bioinformatics 08-10-2016, 03:47 AM
Replies: 1
Views: 1,400
Posted By LeonDK
It turned out to be an invalid header line in the...

It turned out to be an invalid header line in the input VCF file
Forum: Bioinformatics 08-09-2016, 06:40 AM
Replies: 1
Views: 1,400
Posted By LeonDK
bcftools fixref Floating point exception (core dumped)

As described here (https://imputation.sanger.ac.uk/?resources=1) I want to use bcftools +fixref to "convert from Illumina TOP convention to fwd reference strand". However when I run:

bcftools...
Forum: Bioinformatics 08-05-2016, 02:54 AM
Replies: 4
Views: 5,202
Posted By LeonDK
I wrote me a small script to search and identify...

I wrote me a small script to search and identify sample name duplicates and exclude, such that only one is kept for each possible duplicate.

Thanks for input.
Forum: Bioinformatics 08-05-2016, 02:29 AM
Replies: 4
Views: 5,202
Posted By LeonDK
Yes, I was looking for a tool, which could...

Yes, I was looking for a tool, which could identify and remove sample duplicates :)
Forum: Bioinformatics 08-04-2016, 10:22 PM
Replies: 4
Views: 5,202
Posted By LeonDK
VCF to BCF conversion error: [E::bcf_hdr_add_sample] Duplicated sample name

In converting a .vcf file to a .bcf file a get the following error message:
[E::bcf_hdr_add_sample] Duplicated sample name

I am running conversion using bcftools like so:
bcftools convert -O u...
Forum: Bioinformatics 07-07-2016, 02:50 AM
Replies: 0
Views: 1,390
Posted By LeonDK
GWAS state-of-the-art how-to?

Dear all,

Newbie here - So I have embarked on a new journey to the land of GWAS! This means that I now have a plethora of file formats and software tools, that I'll need to absorb. I am hoping for...
Forum: Bioinformatics 07-04-2016, 10:59 PM
Replies: 2
Views: 3,031
Posted By LeonDK
Thank you! For future reference, ...

Thank you!

For future reference,

vcf-subset -c sample1,sample2,sample3 myFile.vcf.gz > mySlicedFile.vcf

did the trick!

and I got vcftools from https://vcftools.github.io/downloads.html
Forum: Bioinformatics 07-04-2016, 04:45 AM
Replies: 2
Views: 3,031
Posted By LeonDK
Split VCF file based on a list of samples

I have a VCF file and a file with a list of samples. I would like to create a new VCF file only containing the samples on the list.

I could write a script, but if someone already created something...
Forum: Bioinformatics 07-04-2016, 04:40 AM
Replies: 3
Views: 3,419
Posted By LeonDK
Ok, thank you.

Ok, thank you.
Forum: Bioinformatics 07-01-2016, 12:33 AM
Replies: 3
Views: 3,419
Posted By LeonDK
Illumina chromosome numbers 0-26 - Meaning of 0?

Hi all,

I am working on a vcf-file, where illumina has encoded the chromosomes in column as 0-26.

I have figured out, that:
1-22 autosomes
23 X
24 Y
25 XY pseudo-autosomal region
26 MT
Forum: Bioinformatics 06-22-2016, 09:49 AM
Replies: 13
Views: 5,431
Posted By LeonDK
You sir, are my new hero! $ cd...

You sir, are my new hero!

$ cd ~/tmp/bcftools/
$ wget https://raw.githubusercontent.com/pd3/bcftools/develop/plugins/fixref.c
$ gcc -fPIC -shared -O2 -I . -I ../htslib/ -o fixref.so version.c...
Forum: Bioinformatics 06-22-2016, 03:25 AM
Replies: 13
Views: 5,431
Posted By LeonDK
I have checked out the "Plugins troubleshooting:"...

I have checked out the "Plugins troubleshooting:" at https://samtools.github.io/bcftools/bcftools.html with no luck.

So far unfortunately, I am stuck. I have written Sanger and the author and I am...
Forum: Bioinformatics 06-21-2016, 11:43 PM
Replies: 13
Views: 5,431
Posted By LeonDK
It's not flying, despite using the stated syntax,...

It's not flying, despite using the stated syntax, I still get
Could not initialize fixref, version string not found

I cannot find any elaboration on the fixref plugin on Sanger. I have tried to...
Forum: Bioinformatics 06-21-2016, 11:05 AM
Replies: 13
Views: 5,431
Posted By LeonDK
Thanks a lot for input GenoMax! It's getting late...

Thanks a lot for input GenoMax! It's getting late in my part of the world, i will continue working on the issue tomorrow...
Forum: Bioinformatics 06-21-2016, 10:41 AM
Replies: 13
Views: 5,431
Posted By LeonDK
Thank you, that worked with respect to getting...

Thank you, that worked with respect to getting fixref.c compiled into fixref.so, like so:
sudo gcc -shared -o fixref.so -fPIC fixref.c

however, unfortunately I am not quite there yet:
$ bcftools...
Forum: Bioinformatics 06-21-2016, 10:28 AM
Replies: 13
Views: 5,431
Posted By LeonDK
Okay, so I got the plugins to install, by going...

Okay, so I got the plugins to install, by going to https://samtools.github.io/bcftools/ and then issuing the following commands:
git clone --branch=develop git://github.com/samtools/htslib.git
git...
Forum: Bioinformatics 06-21-2016, 09:58 AM
Replies: 13
Views: 5,431
Posted By LeonDK
Problems installing bcftools and fixref plugin for using Sanger Imputation Service

Dear all,

I am trying to use the Sanger imputation service (https://imputation.sanger.ac.uk/), but I get the following error:
"Reference allele mismatch at 1:752566 .. REF_SEQ:'G' vs VCF:'A'"
...
Forum: RNA Sequencing 06-18-2015, 09:25 AM
Replies: 8
Views: 2,826
Posted By LeonDK
Ok, so of course I know very well, that there is...

Ok, so of course I know very well, that there is no magic number. In fact pretty much every cut-off we use is arbitrary, especially the infamous 0.05 - Anyhoo...

For publication-purposes it is...
Forum: RNA Sequencing 06-18-2015, 08:55 AM
Replies: 8
Views: 2,826
Posted By LeonDK
Good point! :) So in your opinion, it is...

Good point! :)

So in your opinion, it is sufficient to report the number of mapped reads? E.g. "we included samples with at least 10 mio. mapped reads" or something similar?
Forum: RNA Sequencing 06-18-2015, 01:17 AM
Replies: 8
Views: 2,826
Posted By LeonDK
Hmm... No and yes... Of course if something maps...

Hmm... No and yes... Of course if something maps it (in theory) means that a transcript originated from there. But if I am to use the annotations for GRCh38 for analysis of DEG, than the reads...
Forum: RNA Sequencing 06-18-2015, 01:07 AM
Replies: 2
Views: 2,775
Posted By LeonDK
Okay so I looked extensively around and I found...

Okay so I looked extensively around and I found this gem: http://ocw.mit.edu/courses/biology/7-91j-foundations-of-computational-and-systems-biology-spring-2014/video-lectures/

Just for future...
Showing results 1 to 25 of 69

 


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