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Search: Posts Made By: eeyun
Forum: Bioinformatics 10-01-2013, 01:59 PM
Replies: 3
Views: 2,301
Posted By eeyun
I'm sorry to re-ask the same question again, but...

I'm sorry to re-ask the same question again, but I've noticed another missed variant call using the same above pipeline, and this one I can't figure out based on the base qualities. If anyone can...
Forum: Bioinformatics 09-03-2013, 08:36 AM
Replies: 3
Views: 2,301
Posted By eeyun
Thanks very much for the reply. I had...

Thanks very much for the reply.

I had wondered whether this was a result of the base quality being downgraded by samtools, and therefore not read by varscan. I've tried mpileup with -B and -E,...
Forum: Bioinformatics 08-29-2013, 11:19 AM
Replies: 3
Views: 2,301
Posted By eeyun
VarScan mpileup2snp missing a call - can't figure out why

VarScan mpileup to snp seems to be missing a call

the mpileup file looks like this...
...
Forum: Bioinformatics 06-02-2013, 11:52 AM
Replies: 2
Views: 1,539
Posted By eeyun
removing primer sequences from overlapping amplicons

Hi all -

I'm wondering what methods you'd recommend to remove primer sequences from amplicon sequencing data where multiple amplicons for the same specimen in the same run will overlap. Simply...
Forum: Bioinformatics 05-15-2013, 10:39 AM
Replies: 22
Views: 10,927
Posted By eeyun
Attachment included here to show the variant in...

Attachment included here to show the variant in question.
Forum: Bioinformatics 05-15-2013, 10:38 AM
Replies: 22
Views: 10,927
Posted By eeyun
As far as I can tell, it should be ref = TTCC and...

As far as I can tell, it should be ref = TTCC and alt = T
Forum: Bioinformatics 05-15-2013, 10:32 AM
Replies: 22
Views: 10,927
Posted By eeyun
We are having the same problem with 2.3.5 ...

We are having the same problem with 2.3.5

<pre>#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Sample1...
Forum: Bioinformatics 05-06-2013, 08:51 AM
Replies: 4
Views: 1,737
Posted By eeyun
Thanks for your input. I am hoping to preserve...

Thanks for your input. I am hoping to preserve the coordinates to enable visualization and annotation without too much deviation from our standard practice.
Forum: Bioinformatics 05-06-2013, 08:12 AM
Replies: 4
Views: 1,737
Posted By eeyun
Alignment to a set of custom reference sequences along with standard genome reference

Hi there - any help appreciated here, I'm a relative newbie to NGS evaluation.

I'd like to be able to detect low level deletions of 15bp (or more) in an amplicon-enrichment based assay. We are...
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