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Posts by aadam35411
... Thank you for the explanation, that clears up a lot. Right now I'm working on learning the pipeline to go from the original Illumina sequencing reads (fastq) to a VCF file. I have the two original read files and a copy of hg19, and all the other files I have have been derived from these three files. ...
... In order to perform somatic mutation calling with varscan, I need to run this line: java -jar VarScan.jar somatic normal.pileup tumor.pileup output.basename I was wondering if there is a place to get either a pileup version of hg19 or even a bam file of it in order to put it in the spot for "n ...
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