Page ProgressReportEmde-05-2011

Progress Report (under construction)

Accomplishments in the last six months:

SplazerS:

• redid single end read simulation (compared with GSNAP, BWA)
• added anchored split mapping feature (compared with Pindel)
• added support for SAM input/output
• submitted paper

Ongoing data analysis projects:

• Gene fusions in 454 RNA-Seq data (Lena Feldhahn, Tübingen)
• Targeted resequencing data from human heart, 454 data (Marcel Grunert, MPI)
• Resequencing projects of Ropers department (X-linked mental retardation is done → paper submitted?)

Other:

• Helped Manuel with benchmark paper
• Reviewed ReadDB paper
• Seqan Release 1.3

Goals for the next six months

Will-dos:

• Thesis: Write up split mapping methods and results (possibly also parts of previous work)
• Work on SnpStore (+ write up as much as already possible):
• compare with Dindel, samtools + SRMA/BAQ
• no other tool really does multi-read realignments, but always reads are realigned to candidate "haplotypes" which are built from pairwise alignments and are static (maybe SnpStore worth a paper?)
• possibly improve realignment scoring (reads weighted by quality?)
• add basic 454 indel calling model

Would-like-to-dos:

• With Birte: MultiSplitMapping with STELLAR (maybe with Kathrin Trappe?) (K:yes)
• Integrate allele-separation in SnpStore + add a allele-specific pile up correction --> should increase sensitivity (K: maybe talk to Leon Kuchenbecker)
• check 1000 genome data for retrocopies

Other:

• Lipari Summer School (2.-9.7.)
• EMBL variant detection workshop (18.-20.7.)
• IMPRS retreat (21.-23.7.)
• SeqAn retreat (12.-16.9.)

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