20120423.NGS.Rennes

Knime4Bio a set of custom nodes for the interpretation of NGS data with KNIME. Biogenouest Génomique Rennes 23 avril 2012 Pierre Lindenbaum PhD UMR1087 – Institut du thorax @yokofakunhttp://plindenbaum.blogspot.com

http://commons.wikimedia.org/wiki/File:Calendar-leapyeardate.jpg

http://www.nature.com/news/2011/111005/full/478022a/box/1.html

VCFhttp://bioinf.comav.upv.es/courses/sequence_analysis/snp_calling.html

How do weanalyze/filterthose data ?

Command line Line Command

grep v "PATH" < sample2vcf.tsv |${VARKIT}/scanvcf |${VARKIT}/normalizechrom | Command lineawk F ($3==".") |sort t k1,1 k2,2n k4,4 k5,5 k11,11 |${VARKIT}/samplespersnp sample 11 |awk F ($12=="1") |${VARKIT}/extractinfo t DP |${VARKIT}/extractinfo t GN |${VARKIT}/extractinfo t PRED |${VARKIT}/extractformat t GT |awk F (int($6)>25.0) |awk F (int($13)>10.0) |awk F ($16!="1/1") |awk F ($15!="EXON_SYNONYMOUS" && $15!="GENOMIC" && $15!="INTRON") |groupbygene gene 14 sample 11 |awk F (int($5)==2) |awk F (int($6)==2)

http://code.google.com/p/variationtoolkit/

“command line”A PhD candidate

Did you includeDid we try fix the the results from maximum Polyphen ?number of SNPs per gene ? Can you test with a minimal DEPTH=20 ? Did we ever find this gene ? And with minimal number of affected samples per SNP = 2 ? And with minimal number of affected Can you removesamples per gene = 4 ? all the known SNPs ?

http://www.flickr.com/photos/ohm17/162622755

I want a GUI

http://research.nhgri.nih.gov/software/VarSifter/

Apache Tomcatservlets/jsp SAM-JDK

Java Swing (GUI) based solution

A quick access to the data was needed.http://www.oracle.com/technetwork/database/berkeleydb/overview/index-093405.html

WORKFLOW ENGINE

http://mobyle.pasteur.fr/

http://main.g2.bx.psu.edu/ Galaxy

TAVERNA http://www.taverna.org.uk/

http://en.wikipedia.org/wiki/File:Knime.jpg

http://www.flickr.com/photos/knolleary/6212065238

http://code.google.com/p/knime4bio/

NCBI Entrez

Intersections BED UCSC TABIX bigwig …

WEB SERVICES EMBL STRINGExome Variant Server UNIPROT DAS ….

PREDICTIONS SnpEFFBasic Predictions ….

Interaction with the Client IGVReading the BAM ….

NCBI Protein

Java snippet

Uniprot

Implementing a new node is easy

interface Model { Table[] execute(Table tables[]); }

MerciVincent PorteroChristian DinaEstelle BaronStephanie ChatelMarta SanchezStéphanie BonnaudMatilde KarakachoffRichard RedonHadja EldjouziFrançoise GrosAurore DespresLaetitia DuboscqEric CharpentierSimon LecointeFlogiane SimoretSolena le ScouarnecThe Biostar community

20120423.NGS.Rennes

by Pierre Lindenbaum

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