Elementolab/Personal Medicine Pipeline

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  • mutation analysis 
# alignment

# SNVs
perl /home/ole2001/PROGRAMS/SNPseeqer/SCRIPTS/RNAseq_addMD_split_SNVseeqer.pl --dirs=001,002 --submit=1

# differentially abundant SNVs between tumors and controls
gr "/home/ole2001/PROGRAMS/SNPseeqer/CompareSNVsAlleleFrequencyWithControl -snvfile 001/s_7_sequence.txt.tophat/accepted_hits.bam.MD.sam.SNVs.dbSNP.annot.1KG.kmut.TFBS.Cons.flseq.qs   -readdir 002/s_7_sequence.txt.tophat/accepted_hits.bam.MD.sam_SPLIT/  -chrdata /home/ole2001/PROGRAMS/SNPseeqer/REFDATA/hg19.chrdata -fdr 0.05 "  --name=S001_7 --memory=8g
  • fusion analysis

To summarize multiple fusion analyses 

perl ~/PROGRAMS/SNPseeqer/SCRIPTS/TopHatFusion_summarize_filter.pl

To add - automated blast based filtering of fusions ftp://ftp.ncbi.nlm.nih.gov/blast/documents/web_blast.pl

Retrieved from "https://icb.med.cornell.edu/wiki/index.php/Elementolab/Personal_Medicine_Pipeline"
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