Transcript Report of DTL meeting on NGS variant sharing

Report of DTL meeting on NGS
variant sharing
Leon Mei
LUMC-SASC
NGS data sharing
http://wiki.disc.dtls.nl/index.php/Focus_Meeting:_NGS_data_sharing_and_repository
Typical clinical NGS data flow
Patient
registration
Geneticist's
diagnosis
Exome
sequencing
Filtering
variants
Result variants
Raw and
intermediate files
Storage of anonymized raw
seq data and meta data
DVD
Analysis at
local cluster
Variant frequency
sharing and querying
LOVD
Cafe Variome
Cafe Variome
Center for Personalized Cancer Treatment
EBI-EGA
NFU data strategy
Other than human data
NGS data requirement – LUMC
NGS data requirement
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3 billion bases per Genome
1KG, GoNL, Leiden Longevity Study,
Rotterdam study
© The economist
© Eline Slagboom
Patient
registration
Geneticist's
diagnosis
Exome
sequencing
DVD
Storage of anonymized raw
seq data and meta data
Analysis at
local cluster
Variant frequency
sharing and querying
Pipeline metadata,
Clinical data
@local backup
Intermediate files
Research data
@EBI-EGA
Makefile pipeline
●
Shell script
1 bwa aln -t 8 $reference $i > $i.sai
2 bwa samse $reference $i.sai $i > $i.sam
3 samtools view −bt $reference −o $i.bam $i.sam
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Makefile
1 %.sai : %.fq
2 $(BWA) aln −t $(THREADS) $( call MKREF, $@) $< > $@
3
4 %.sam: %.sai %.fq
5 $(BWA) samse $( call MKREF, $@) $ˆ > $@
6
7 %.bam: %.sam
8 $(SAMTOOLS) view −bt $( call MKREF, $@) −o $@ $<
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clean:
rm -rf *.fastqc *.stats *.tex *.sam *.sai *.flagstat *.bai \
*.pileup *.synced.$(FASTQ_EXTENSION) *.wig *.ontarget *.bed *.bcf \
*tar.gz *ti-tv.txt *.covPerTarget *.hsMetrics ...
NGS data requirement
BBMRI Biobank-based Integrative
Omics Studies (BIOS)
6 biobanks, thousands samples
4,000
4,000
4,000
Grid
Cloud
4K RNAseq data management
3
3
2
1
2
1
#1 data upload
#2 verification, backup
3
2
#3 process runs
BIOS metadata DB
HPC cloud based analysis
Acknowledgement
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DTL focus meeting
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BBMRI BIOS
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Johan den Dunnen, Ies Nijman, Ivo Fokkema, Martijn Vermaat,
Morris Swertz, Justin Paschall, Anthony J Brookes, Hendrik-Jan
Megens
Michiel van Galen, Maarten van Iterson, Matthijs Moed, Jan Bot,
Jeroen van Rooij, Marijn Verkerk, Freerk van Dijk, Bas
Heijmans, Peter-Bram 't Hoen, Rene Luijk, Lude Franke,
Dasha Zhernakova, Patrick Deelen,Rick Jansen, Aaron
Isaacs, Joyce van Meurs, Morris Swertz
LUMC
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Jeroen Laros, Wibowo Arindrarto, Wai Yi Leung, Peter van't Hof
Backup slides