[GSoC] GSoC 2014 queries and inputs

[Francesco Strozzi]

Hi Ujjwal,
there is no official template, I would suggest to organize the proposal in
sections, one describing yourself (experience, passions, skills etc.), one
giving the background for the proposal and one describing your actual work
plan. This one should be where you concentrate the most, please try to
organize the work plan in weeks and set also deliverables for each period.

Francesco


On Wed, Mar 19, 2014 at 5:23 PM, Ujjwal Thaakar <ujjwalthaakar at gmail.com>wrote:

> Is there a template for the application proposal?
>
>
> On 19 March 2014 19:56, Fields, Christopher J <cjfields at illinois.edu>
> wrote:
>
> >  On Mar 19, 2014, at 8:28 AM, Artem Tarasov <lomereiter at gmail.com>
> wrote:
> >
> >   On Tue, Mar 18, 2014 at 11:44 PM, Ujjwal Thaakar <
> > ujjwalthaakar at gmail.com> wrote:
> >
> >> What's the difference between SAM and VCF?
> >
> >
> >  SAM: mapping software aligns reads against the reference genome (and its
> > reverse-complement) and writes to SAM/BAM file information about best
> > alignment of each read (to which strand it aligned, what are the
> > differences compared to the reference, and so on)
> >
> >  VCF: not reads but positions on the reference genome are considered, and
> > each record contains information about whether there's variability at a
> > position. They are produced from SAM files by considering reads
> overlapping
> > each position - if statistically significant number of reads have a base
> > different from the reference (or an insertion/deletion), this is
> probably a
> > true mutation which might have biological significance as well.
> >
> >  For JRuby, I'd recommend using Picard. No need to reinvent the wheel.
> > Plus, you might also want to support the binary counterpart, BCF format.
> >
> >
> >  --
> > Artem
> >
> >
> > Yep, if planning on going through jvm then Picard is nice and supports
> VCF
> > (and BCF it seems).  No CRAM support, but there is this:
> >
> >     https://github.com/enasequence/cramtools
> >
> >  (section on picard integration)
> >
> >  chris
> >
>
>
>
> --
> Thanks
> Ujjwal
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-- 

Francesco Strozzi