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Algorithm to implement Fraction and Copy number Estimate from Tumor/normal Sequencing.
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no output #138

Closed lihm1 closed 5 years ago

lihm1 commented 5 years ago 
(R) [lccc@HPC-login out]$ zcat 909-WCMC11.out.gz 
Chromosome,Position,Ref,Alt,File1R,File1A,File1E,File1D,File2R,File2A,File2E,File2D

I do not know why my otput is nothing. My code is ./snp-pileup -g -q15 -Q20 -P100 -r25,0 common_all_20180418.vcf.gz\ ${path1}/909-WCMC11.out.gz \ ${path2}/SRR3146752.sorted.marked.BQSR.bam \ ${path2}/SRR3146775.sorted.marked.BQSR.bam can you tell me how to correct? Thanks!