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Forum: Literature Watch 03-13-2016, 08:46 PM
Replies: 41
Views: 29,645
Posted By etal
Deepak, another user reported this issue and...

Deepak, another user reported this issue and found that it was due to a bug in Pysam 0.9:
https://github.com/etal/cnvkit/issues/86

Your original command should work for you if you are able to...
Forum: Literature Watch 03-12-2016, 06:10 PM
Replies: 41
Views: 29,645
Posted By etal
You can skip bedcov with the -c/--count-reads...

You can skip bedcov with the -c/--count-reads option; it uses a different method to calculate read depths but should give similar results.

Also, if you've successfully built the target and...
Forum: Literature Watch 03-11-2016, 05:13 PM
Replies: 41
Views: 29,645
Posted By etal
The antitarget BED file has "chr" because...

The antitarget BED file has "chr" because "access-5k-mappable.hg19.bed" has chr. You could build an access file for GRCh37 using "cnvkit.py access", but it would probably be quicker for you to just...
Forum: Literature Watch 03-11-2016, 11:09 AM
Replies: 41
Views: 29,645
Posted By etal
Deepak, I notice your antitarget BED chromosomes...

Deepak, I notice your antitarget BED chromosomes names start with "chr" but your target BED chromosome names do not. Which names are in your BAM file? (I'm guessing "chr", like hg19, based on the...
Forum: Literature Watch 03-10-2016, 12:41 PM
Replies: 41
Views: 29,645
Posted By etal
DrWorm: The SEG parser handles 5- or 6-column...

DrWorm: The SEG parser handles 5- or 6-column tables like the one you've posted. I wonder if the ValueError is due to the "WARNING" message from R getting fed to the SEG parser in CNVkit, just before...
Forum: Literature Watch 03-10-2016, 12:35 PM
Replies: 41
Views: 29,645
Posted By etal
Deepak: I haven't been able to replicate the...

Deepak: I haven't been able to replicate the error. Are you sure you used a valid BED file, i.e. my_targets.bed is a 4-column BED file that you've preprocessed with "cnvkit.py target"? The error...
Forum: Literature Watch 03-09-2016, 03:25 PM
Replies: 41
Views: 29,645
Posted By etal
Sorry for the trouble. Could you post the first...

Sorry for the trouble. Could you post the first few lines of the output table and the version of CNVkit you're using (try "cnvkit.py version")?

If you're able to load the PSCBS package in R, could...
Forum: Literature Watch 03-08-2016, 07:33 AM
Replies: 41
Views: 29,645
Posted By etal
Hi Deepak, The sequence IDs are the...

Hi Deepak,

The sequence IDs are the chromosome names in your reference genome and the first column of your BED file. For the human genome the first chromosome might be "1" or "chr1" depending on...
Forum: Literature Watch 05-14-2015, 10:08 AM
Replies: 41
Views: 29,645
Posted By etal
The mapping quality threshold is hard-coded to...

The mapping quality threshold is hard-coded to only exclude unmapped or ambiguously mapped reads, see here:
https://github.com/etal/cnvkit/blob/master/cnvlib/coverage.py#L115

Just change the -Q...
Forum: Literature Watch 05-11-2015, 04:15 PM
Replies: 41
Views: 29,645
Posted By etal
Hi wisekh, The LOH functionality in CNVkit...

Hi wisekh,

The LOH functionality in CNVkit is described here:
http://cnvkit.readthedocs.org/en/latest/plots.html#scatter

However, the "calls" are simply displayed visually -- the variant...
Forum: Literature Watch 04-06-2015, 11:05 AM
Replies: 41
Views: 29,645
Posted By etal
What files were generated by the second run, if...

What files were generated by the second run, if any? Can you show me the status messages or any errors that were printed?

When you run CNVkit with a reference, you don't need the "--targets",...
Forum: Literature Watch 03-12-2015, 02:20 PM
Replies: 41
Views: 29,645
Posted By etal
Hi Ies, Sorry I missed your post earlier....

Hi Ies,

Sorry I missed your post earlier. There isn't a verbose logging mode in CNVkit, but the messages on standard error are fairly verbose already and should always report when there is an...
Forum: Literature Watch 02-26-2015, 01:33 PM
Replies: 41
Views: 29,645
Posted By etal
I've added the "-c/--count" option from the...

I've added the "-c/--count" option from the "coverage" command to the "batch" options as well. If you installed CNVkit from the GitHub repo (http://github.com/etal/cnvkit), you can get the latest by...
Forum: Literature Watch 02-25-2015, 10:25 AM
Replies: 41
Views: 29,645
Posted By etal
Hi Marlous, Thanks for reporting this. Can...

Hi Marlous,

Thanks for reporting this. Can you show me the commands you used to trigger this error, including any special options you used? Are your BAM files definitely in BAM format, and e.g....
Forum: Literature Watch 02-23-2015, 05:37 PM
Replies: 41
Views: 29,645
Posted By etal
Yes, CNVkit is designed for hybrid capture target...

Yes, CNVkit is designed for hybrid capture target panels like those of Illumina, Agilent and Nimblegen. For best results from amplicon-based targeted resequencing, you should probably use another...
Forum: Literature Watch 02-18-2015, 01:45 PM
Replies: 41
Views: 29,645
Posted By etal
The BAM files available on your server or under...

The BAM files available on your server or under your account (however you've set it up) should be visible under either field in the input form, and you should be able to select the files you want for...
Forum: Literature Watch 02-04-2015, 09:37 AM
Replies: 41
Views: 29,645
Posted By etal
Hi Jasper, If you would like to quickly get...

Hi Jasper,

If you would like to quickly get started without doing any technical work, I recommend the DNAnexus app (https://platform.dnanexus.com/app/cnvkit_batch), which is essentially complete...
Forum: Bioinformatics 12-28-2014, 01:28 PM
Replies: 2
Views: 1,762
Posted By etal
THetA2 can infer absolute copy number from read...

THetA2 can infer absolute copy number from read depth: http://compbio.cs.brown.edu/projects/theta/

It runs using the segmentation output of BIC-seq, ExomeCNV, EXCAVATOR or CNVkit, and infers the...
Forum: Bioinformatics 12-08-2014, 03:14 PM
Replies: 1
Views: 1,787
Posted By etal
You can use a program like CoNIFER...

You can use a program like CoNIFER (http://conifer.sourceforge.net/) or cn.MOPS (http://www.bioinf.jku.at/software/cnmops/) to process the samples as a cohort. These programs each use a statistical...
Forum: Bioinformatics 12-05-2014, 10:49 PM
Replies: 1
Views: 3,190
Posted By etal
Mentioned in another thread: I think...

Mentioned in another thread:



I think this is the sort of variant caller I was looking for.
Forum: Bioinformatics 11-26-2014, 05:03 PM
Replies: 1
Views: 3,190
Posted By etal
Lightbulb Tumor-only variant calling

I'm attempting to call SNVs in tumor samples without a paired normal sample. Some of these tumor samples can have low purity, so the allelic frequency of somatic variants is much lower than the .5...
Forum: Literature Watch 10-30-2014, 03:48 PM
Replies: 41
Views: 29,645
Posted By etal
Post CNVkit: Copy number detection and visualization for targeted sequencing using off-tar

CNVkit is a software toolkit to infer and visualize copy number from targeted DNA sequencing data. It is designed for use with hybrid capture, including both whole-exome and custom target panels, and...
Forum: General 10-31-2013, 11:01 AM
Replies: 1
Views: 4,616
Posted By etal
The 1000G and 5400ESP projects used different...

The 1000G and 5400ESP projects used different pipelines for sequencing, read mapping and and variant calling, so at least some of the major discrepancies between the listed allele frequencies are due...
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