SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 25 of 36
Search took 0.00 seconds.
Search: Posts Made By: ekg
Forum: Bioinformatics 07-10-2013, 11:53 PM
Replies: 8
Views: 9,998
Posted By ekg
There is also vcfintersect:...

There is also vcfintersect: https://github.com/ekg/vcflib#vcfintersect

It works with both BED files and VCF files, and can generate inverse intersections (allowing you to find things that are not...
Forum: Bioinformatics 01-29-2013, 03:07 PM
Replies: 13
Views: 14,588
Posted By ekg
@mattanswers This sounds like a job for your...

@mattanswers This sounds like a job for your favorite aligner. For short sequences, you can use smith-waterman (https://github.com/ekg/smithwaterman) but for bigger stuff I'd use something like blat...
Forum: Bioinformatics 01-23-2013, 09:28 AM
Replies: 9
Views: 5,669
Posted By ekg
@Andrea Non ti preoccupare, parlo italiano. ...

@Andrea

Non ti preoccupare, parlo italiano.

Mi sembra che si manca zlib: http://stackoverflow.com/questions/1632201/error-deflate-and-inflate-with-zlib

Zlib e' installato nella tua sistema?
Forum: Bioinformatics 12-21-2012, 12:17 AM
Replies: 11
Views: 4,199
Posted By ekg
Just to be clear, the current focus of Tangram is...

Just to be clear, the current focus of Tangram is mobile element insertions. CNV detection is a future development.
Forum: Bioinformatics 12-20-2012, 11:02 PM
Replies: 11
Views: 4,199
Posted By ekg
The new MEI detector is called Tangram, and it...

The new MEI detector is called Tangram, and it has been released under an MIT license: https://github.com/jiantao/Tangram!

Please inform the author, Jiantao Wu, if you encounter any issues in...
Forum: Bioinformatics 12-20-2012, 12:55 AM
Replies: 8
Views: 4,431
Posted By ekg
Another thought about the figure in the paper. ...

Another thought about the figure in the paper. I've done a lot of testing with GATK, freebayes, and samtools, and I've never seen samtools generate a curve like that in the figure.

Also, I'm...
Forum: Bioinformatics 12-20-2012, 12:44 AM
Replies: 4
Views: 5,339
Posted By ekg
I believe I know what's going on here. In...

I believe I know what's going on here.

In the old versions, freebayes was designed to behave like gigabayes/bambayes, which used BQ and MQ filters to remove a lot of low-quality reads.

However,...
Forum: Bioinformatics 12-20-2012, 12:40 AM
Replies: 4
Views: 5,339
Posted By ekg
I'd guess this is a problem with BAM format...

I'd guess this is a problem with BAM format changes or the specific (older) version which you were using, but I'm not sure. This sounds pretty strange--- we don't see this at all in testing and if...
Forum: Bioinformatics 12-20-2012, 12:37 AM
Replies: 7
Views: 8,132
Posted By ekg
As aeonism says, the QUAL represents the...

As aeonism says, the QUAL represents the probability of polymorphism at the site, not the probability that the genotype call which is described is correct. There are various ways to attempt to get...
Forum: Bioinformatics 12-20-2012, 12:19 AM
Replies: 11
Views: 4,199
Posted By ekg
I'm in Chip's old Lab (Gabor Marth's group). A...

I'm in Chip's old Lab (Gabor Marth's group). A member of our group has developed a new mobile element insertion detector. It's performing well in tests but I'm not sure if it's ready for public...
Forum: Bioinformatics 12-19-2012, 11:44 PM
Replies: 12
Views: 8,060
Posted By ekg
@Zam, this looks great! I'm looking forward to...

@Zam, this looks great! I'm looking forward to reading it.
Forum: Bioinformatics 12-19-2012, 06:34 AM
Replies: 8
Views: 4,431
Posted By ekg
Oh! I see. I should have examined the...

Oh! I see. I should have examined the manuscript. Nice work!

A few comments, mostly focused on the comparison in the draft:

When comparing the results of the various variant callers, how did...
Forum: Bioinformatics 12-19-2012, 04:33 AM
Replies: 4
Views: 1,412
Posted By ekg
If you have a haploid sample, and only one...

If you have a haploid sample, and only one sample, and the VCF reflects that fact (e.g. you called with freebayes --ploidy 1) then you can use vcfgeno2haplo...
Forum: Bioinformatics 12-19-2012, 04:30 AM
Replies: 9
Views: 5,669
Posted By ekg
I wrote something in C++...

I wrote something in C++ (https://github.com/ekg/vcflib/blob/master/vcfbreakmulti.cpp):

% vcfbreakmulti --help
usage: vcfbreakmulti [options] [file]

If multiple alleles are specified in a...
Forum: Bioinformatics 12-19-2012, 04:27 AM
Replies: 34
Views: 11,970
Posted By ekg
Have you tried bamtools? I believe the command...

Have you tried bamtools? I believe the command is:

bamtools convert -in file1.bam -in file2.bam ... -format fastq >reads.fq
Forum: Bioinformatics 12-19-2012, 04:15 AM
Replies: 12
Views: 8,060
Posted By ekg
Also, you can use vcfgeno2haplo...

Also, you can use vcfgeno2haplo (https://github.com/ekg/vcflib/blob/master/vcfgeno2haplo.cpp) with an arbitrarily large window size to generate a consensus fasta sequence from the output.

If you...
Forum: Bioinformatics 12-19-2012, 04:11 AM
Replies: 12
Views: 8,060
Posted By ekg
Why not use freebayes? It's designed to support...

Why not use freebayes? It's designed to support haploids and polyploids (use the --ploidy option).
Forum: Bioinformatics 12-19-2012, 03:01 AM
Replies: 8
Views: 4,431
Posted By ekg
Can SNPSVM be used to call SNPs in multiple...

Can SNPSVM be used to call SNPs in multiple samples? If so, I'll include it in the comparisons I've developed for multi-sample variant detection.

When you say "more accurate" do you mean lower FP...
Forum: Bioinformatics 12-19-2012, 02:57 AM
Replies: 2
Views: 1,538
Posted By ekg
I'm planning on adding BCF support to vcflib. ...

I'm planning on adding BCF support to vcflib. Patches are welcome!
Forum: Bioinformatics 12-05-2012, 04:00 AM
Replies: 17
Views: 13,145
Posted By ekg
It appears that samtools is not using reads which...

It appears that samtools is not using reads which are not marked as proper pairs. This was my problem, and it led me to this thread. I fixed it with bamtools resolve.
Forum: Bioinformatics 12-05-2012, 03:59 AM
Replies: 1
Views: 1,286
Posted By ekg
Some tests I just did show that samtools mpileup...

Some tests I just did show that samtools mpileup only works for proper pairs. Can anyone else confirm this?

I was not able to call any variants until I marked the pairs with bamtools resolve.
Forum: Bioinformatics 12-05-2012, 03:18 AM
Replies: 1
Views: 1,207
Posted By ekg
What do you get with other snp+indel methods...

What do you get with other snp+indel methods (e.g. freebayes or GATK)?
Forum: Bioinformatics 12-05-2012, 02:55 AM
Replies: 17
Views: 13,145
Posted By ekg
As can freebayes. By default it outputs all...

As can freebayes. By default it outputs all sites of even extremely low confidence, P(site polymorphic | data) >= 0.0001 (parameter -P --pvar).

The intent is that users filter their results...
Forum: Bioinformatics 10-16-2012, 03:05 AM
Replies: 4
Views: 2,887
Posted By ekg
I don't have the input data available, but this...

I don't have the input data available, but this is exactly the kind of thing which bamleftalign is designed to resolve. Did it work for you?
Forum: Bioinformatics 10-01-2012, 06:21 AM
Replies: 2
Views: 646
Posted By ekg
I have been using wgsim for some time in a...

I have been using wgsim for some time in a testing context. However, I don't allow it to simulate reference-relative mutations. I do this with mutatrix (https://github.com/ekg/mutatrix), a...
Showing results 1 to 25 of 36

 


All times are GMT -8. The time now is 01:59 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2018, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO