Elementolab/RNA-seq variant analysis pipeline

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  • To summarize variants obtained from analysis of TopHat aligned reads, focusing on cancer genes ONLY and with some coverage, mutation frequency, BLOSUM62, etc filters: 
perl ~/PROGRAMS/SNPseeqer/SCRIPTS/findMostFrequentSNVs.pl --samples=sample_info.txt  --canceronly=1  --mincov=10 --minallfreq=0.25 --bl62min=1 \ 
   --sense=1 --maxqspv=0.05 | tee all_samples_variants.txt
  • To transform the variant file into a matrix 
perl ~/PROGRAMS/SNPseeqer/SCRIPTS/addSNVsToFusionTable.pl --snvfile=all_samples_variants.txt > all_samples_variants_table.txt
  • To draw a mutation heatmap 
draw_expression_heatmap.pl --matrix=all_samples_variants_table.txt --draw=open --minmax=1 --xright=100 --drawscale=0
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