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Forum: RNA Sequencing 04-09-2014, 02:35 PM
Replies: 5
Views: 2,340
Posted By grakocevic
Overlap shouldn't be the issue. I'm not...

Overlap shouldn't be the issue.

I'm not sure what the filter the core is referring to (probably Illumina's chastity), but whatever it is, 50% failure is not normal. Try running FastQC on your...
Forum: Bioinformatics 02-19-2014, 07:25 AM
Replies: 3
Views: 3,646
Posted By grakocevic
You should check the Filter column in the VCF. ...

You should check the Filter column in the VCF.
Filtering variants in a VCF usually doesn't mean deleting them, but rather writing something in that column.
Anything that is not '.' or 'PASS'...
Forum: Bioinformatics 02-15-2014, 02:56 PM
Replies: 9
Views: 2,729
Posted By grakocevic
What is the analysis and the pipeline you plan on...

What is the analysis and the pipeline you plan on using? If it's anything that can make use of the read groups (like gatk bqsr) you might want to align separately and merge the bam files (if you even...
Forum: Bioinformatics 02-15-2014, 02:48 PM
Replies: 3
Views: 3,646
Posted By grakocevic
It filters the variants. Let's start from...

It filters the variants.

Let's start from the plain old "hard" filters as you're probably used to.
We have a bunch of metrics for each variant, e.g. call quality, coverage depth at the position,...
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