Hi all,
I used varscan2.3.2 to study groups of normal/tumor matched data sets. I used java -jar Varscan2.3.2 somatic [normal pileup] [tumor pileup]. It outputs about 9,000 indels, of which most of them are reported as Germline and about one hundred of them were LOH or Somatic.
This is my first exome-sequencing project. Does any one has an idea what happened to predict so many indels? BTW, I used bwa to map the reads and duplicates were removed before SNV call.
Thank you.
I used varscan2.3.2 to study groups of normal/tumor matched data sets. I used java -jar Varscan2.3.2 somatic [normal pileup] [tumor pileup]. It outputs about 9,000 indels, of which most of them are reported as Germline and about one hundred of them were LOH or Somatic.
This is my first exome-sequencing project. Does any one has an idea what happened to predict so many indels? BTW, I used bwa to map the reads and duplicates were removed before SNV call.
Thank you.
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