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Forum: Bioinformatics 07-11-2014, 06:31 AM
Replies: 2
Views: 2,942
Posted By oiiio
Converting a VCF with SNPs and indels to BED format

Does anyone know of tools or have custom scripts (aside from "vcf2bed") that are able to convert between a VCF containing both indels and SNPs into BED format? The tricky part is creating the...
Forum: Bioinformatics 06-09-2014, 06:31 AM
Replies: 23
Views: 4,758
Posted By oiiio
We had the command on this GCAT page work: ...

We had the command on this GCAT page work:

http://www.bioplanet.com/gcat/reports/530/variant-calls/illumina-100bp-pe-exome-150x/isaac-isaac/compare-156-adsqyilqlu-571/group-read-depth
Forum: Bioinformatics 01-29-2014, 12:12 PM
Replies: 2
Views: 1,705
Posted By oiiio
*.asc files from capillary sequencing

I've got a number of *.asc files from some capillary seqeuencing, in which the README proclaims the following format. If anyone has experience with this format, I'd really like to understand how the...
Forum: Bioinformatics 12-06-2013, 08:04 AM
Replies: 0
Views: 1,257
Posted By oiiio
Has anyone tried comparing accuracy using different library preps?

Has anyone done variant comparisons between different library preps for exomes? Is this a dumb question?

It would be particularly awesome if someone already has this data in a BioPlanet.com/GCAT...
Forum: Bioinformatics 06-10-2013, 02:10 PM
Replies: 23
Views: 4,758
Posted By oiiio
After downloading the reference I'm now hitting...

After downloading the reference I'm now hitting this error:


2013-06-10 17:52:33 [0x11d36a0] __gnu_parallel:sort for 64000000 elements
terminate called recursively
terminate called...
Forum: Bioinformatics 06-10-2013, 11:30 AM
Replies: 23
Views: 4,758
Posted By oiiio
Thanks I'm downloading it now, although I wonder...

Thanks I'm downloading it now, although I wonder if this download will finish before my indexing command...

Even though it looks like the downloadable ref is based on the same UCSC hg19 I am...
Forum: Bioinformatics 06-10-2013, 11:04 AM
Replies: 23
Views: 4,758
Posted By oiiio
So I realized that the FASTQ names must be...

So I realized that the FASTQ names must be specifically named as lane1_read1.fastq lane1_read2.fastq

Now just trying to index the hg19 reference with isaac-sort-reference . Seems to be taking...
Forum: Bioinformatics 06-06-2013, 05:28 PM
Replies: 23
Views: 4,758
Posted By oiiio
A working command line for Illumina's iSAAC ?

I just got hold of the iSAAC aligner from Illumina, but it seems to use a very different type of command line than most of the other aligners I have used, particularly when specifying a FASTQ. Does...
Forum: Bioinformatics 05-21-2013, 09:26 AM
Replies: 9
Views: 1,437
Posted By oiiio
@abi There is actually a field describing...

@abi

There is actually a field describing the exact command line used (although it is dependent on the uploader to fill in ). For example you should see this in the top right of the report:
...
Forum: Bioinformatics 05-17-2013, 08:40 AM
Replies: 9
Views: 1,437
Posted By oiiio
@id0 I also suggest you play around with...

@id0

I also suggest you play around with GCAT on bioplanet.com, as they have variant calling benchmarks for various softwares. What you might find interesting in particular is a plot showing indel...
Forum: Bioinformatics 05-16-2013, 09:15 AM
Replies: 2
Views: 827
Posted By oiiio
Well... is there a reason you must use SOAP? Have...

Well... is there a reason you must use SOAP? Have you tried different programs like BWA?
Forum: Bioinformatics 05-14-2013, 04:12 PM
Replies: 16
Views: 2,840
Posted By oiiio
What are your read lengths? If 75bp+ I'd...

What are your read lengths? If 75bp+ I'd recommend re-doing the whole thing with BWA-MEM which may fix your sampe problem. Not to mention that BWA-MEM is an improvement in my opinion, based on some...
Forum: Bioinformatics 05-14-2013, 11:39 AM
Replies: 3
Views: 2,575
Posted By oiiio
@mrood Check out these alignment benchmarks...

@mrood

Check out these alignment benchmarks for some different popular tools (BWA, Bowtie2, Novoalign) here:
...
Forum: Bioinformatics 05-09-2013, 06:25 PM
Replies: 0
Views: 818
Posted By oiiio
phasing across reads

Hey all,

I wanted to ask if anyone knows methods for genotype phasing across reads? For example, if two SNPs are on a single read then we can phase to one of the parents where read came from. So...
Forum: Bioinformatics 05-01-2013, 08:26 AM
Replies: 16
Views: 1,497
Posted By oiiio
I've not tried SOAP2 actually, but I have seen a...

I've not tried SOAP2 actually, but I have seen a bunch of comparisons of variant calling pipelines using the other ones you mentioned:
...
Forum: Bioinformatics 05-01-2013, 08:05 AM
Replies: 16
Views: 1,497
Posted By oiiio
which aligners trade off between SNP discovery...

which aligners trade off between SNP discovery and indels/CNVs ?? Except in some types of indels, this is certainly a problem at the level of entire pipeline..
Forum: Bioinformatics 04-30-2013, 08:11 AM
Replies: 16
Views: 1,497
Posted By oiiio
and see GCAT for benchmarks of different tools :)...

and see GCAT for benchmarks of different tools :)

http://www.bioplanet.com/gcat
Forum: Bioinformatics 04-26-2013, 11:31 AM
Replies: 4
Views: 1,290
Posted By oiiio
just wanted to say that novosort (novocraft.com)...

just wanted to say that novosort (novocraft.com) is probably the fastest read sorting I have seen.

In second place is the OpenGE's mergesort function which is open source...
Forum: Bioinformatics 04-24-2013, 06:43 AM
Replies: 4
Views: 6,370
Posted By oiiio
There is a free website tool called GCAT (Genome...

There is a free website tool called GCAT (Genome Comparison and Analytic Testing) that is designed to answer these types of questions without qualitative speculation.

For example, to compare TMAP...
Forum: Bioinformatics 04-23-2013, 10:15 AM
Replies: 7
Views: 3,723
Posted By oiiio
I would also recommend BWA-MEM for large indels....

I would also recommend BWA-MEM for large indels. You can see the GCAT benchmarks for BWA-MEM and other aligners on large indel containing samples for 150bp paired end reads here...
Forum: Bioinformatics 04-21-2013, 06:38 PM
Replies: 1
Views: 915
Posted By oiiio
bioplanet.com has a benchmarks on pipelines in...

bioplanet.com has a benchmarks on pipelines in variant calling with a number of publicly available results for you to look at:
...
Forum: Bioinformatics 04-21-2013, 06:32 PM
Replies: 3
Views: 2,472
Posted By oiiio
Here are a BUNCH of benchmarks on bowtie2 over a...

Here are a BUNCH of benchmarks on bowtie2 over a number of different sequencing platforms

http://www.bioplanet.com/gcat/report-list/public-1/search-bowtie
Forum: Bioinformatics 04-15-2013, 06:44 AM
Replies: 14
Views: 4,489
Posted By oiiio
This is a good point, and I think it would be...

This is a good point, and I think it would be very interesting to see how the alignment reports change with simulator as well. Comparing simulators that use and don't use that kind of error model...
Forum: Bioinformatics 04-14-2013, 06:19 PM
Replies: 14
Views: 4,489
Posted By oiiio
The inner distance for paired end is always 300bp...

The inner distance for paired end is always 300bp (so a template size of 500bp for 100bp reads)

The small indel rate has sizes 1-10bp, and the large indel rate is 10-24bp

Looking forward to...
Forum: Bioinformatics 04-14-2013, 08:43 AM
Replies: 94
Views: 138,439
Posted By oiiio
I started to reply in adaptivegenome's purposed...

I started to reply in adaptivegenome's purposed thread here: http://seqanswers.com/forums/showthread.php?p=101688#post101688
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