[GSoC] GSoC 2014 queries and inputs

[Ujjwal Thaakar]

I've uploaded a first very rough draft of my proposal. I know I got a
little late on this :(
Please go through it and tell me where I can improve :)
https://www.google-melange.com/gsoc/proposal/review/student/google/gsoc2014/ujjwalt/5675163626504192


On 20 March 2014 14:13, Francesco Strozzi <francesco.strozzi at gmail.com>wrote:

> 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
>> _______________________________________________
>> GSoC mailing list
>> GSoC at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/gsoc
>>
>
>
>
> --
>
> Francesco Strozzi
>



-- 
Thanks
Ujjwal