Alice:Exome Sequencing Analysis/FengLab livertumor

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Feng lab mouse liver tumor exome sequencing[edit]

  • Two batch of exome sequencing done by the Feng lab
  • exome varient calling pipeline used: GATK & freebayes (see script below)
First batch of data set:
location on genome-miner:
/home/zhl002/media/LTS_60T/SeqStore2015/Feng_151216
P608 and P610 are PTEN hepatocyte specific knockout mice.
        P608-tumor and P608-tail are tumor and tail samples from P608.
        P610-tumor and P610-tail are tumor and tail samples from P610.
D634 and D642 are PTEN and SHP2 hepatocyte specific knockout mice.
        D634-tumor and D634-tail are tumor and tail samples from D634.
        D642-tumor and D642-tail are tumor and tail samples from D642.
Second batch of data set:
location on genome-miner:
/home/zhl002/media/LTS_60T/SeqStore2016/Feng_160222
tumor sample from liver of 8 months old mice injected DEN (carcinogen)
two pair samples  (A50-tumor, A50-Tail, A43-Tumor, A43-Tail)
two tumor samples (A146-tumor, A149-tumor)