FFPE

5-tool SomaticSeq Consensus

• FFPE-MSDUK-Consensus - FFX_IL_1h

• FFPE-MSDUK-Consensus - FFX_IL_2h

• FFPE-MSDUK-Consensus - FFX_IL_6h

• FFPE-MSDUK-Consensus - FFX_IL_24h

  • MuTect2 re-run after it failed the first time.

  • SomaticSeq Consensus

• FFPE-MSDUK-Consensus - FFX_GZ_1h

• FFPE-MSDUK-Consensus - FFX_GZ_6h

• FFPE-MSDUK-Consensus - FFX_GZ_24h

FFG BAM files did not have @RG in the header (thus no SM). They had to be reheadered first, e.g., Picard_AddOrReplaceReadGroups FFG_IL_T_24h.bwa.dedup.bam. The resulting BAM files have file names like FFX_GZ_T_1h_1.bwa.dedup.NewSM.bam

• FFPE-MSDUK-Consensus - FFG_IL_1h

  • Redo MuTect2, SomaticSeq

• FFPE-MSDUK-Consensus - FFG_IL_2h

  • Redo MuTect2, SomaticSeq

• FFPE-MSDUK-Consensus - FFG_IL_6h

  • Redo MuTect2, VarDict, SomaticSeq

• FFPE-MSDUK-Consensus - FFG_IL_24h

  • Redo MuTect2, SomaticSeq

• FFPE-MSDUK-Consensus - FFG_GZ_1h

  • Redo VarDict, SomaticSeq

• FFPE-MSDUK-Consensus - FFG_GZ_2h

  • Redo VarDict, SomaticSeq

• FFPE-MSDUK-Consensus - FFG_GZ_6h

  • Redo VarDict, SomaticSeq

• FFPE-MSDUK-Consensus - FFG_GZ_24h

• FFPE-MSDUK-Consensus - FFX_IL_T_1h_1_vs_WES_IL_N_1

• FFPE-MSDUK-Consensus - FFX_IL_T_2h_1_vs_WES_IL_N_1

• FFPE-MSDUK-Consensus - FFX_IL_T_6h_1_vs_WES_IL_N_1

• FFPE-MSDUK-Consensus - FFX_IL_T_24h_1_vs_WES_IL_N_1

• FFPE-MSDUK-Consensus - FFX_GZ_T_1h_1_vs_WES_IL_N_1

• FFPE-MSDUK-Consensus - FFX_GZ_T_6h_3_vs_WES_IL_N_1

• FFPE-MSDUK-Consensus - FFX_GZ_T_24h_1_vs_WES_IL_N_1

• FFPE-MSDUK-Consensus - FFG_IL_1h vs. WGS_IL_N_1

• FFPE-MSDUK-Consensus - FFG_IL_2h vs. WGS_IL_N_1

  • Redo SomaticSeq

• FFPE-MSDUK-Consensus - FFG_IL_6h vs. WGS_IL_N_1

• FFPE-MSDUK-Consensus - FFG_IL_24h vs. WGS_IL_N_1

  • Redo MuTect2, VarDict, MuSE, SomaticSeq

• FFPE-MSDUK-Consensus - FFG_GZ_1h vs. WGS_IL_N_1

  • Redo VarDict, SomaticSeq

• FFPE-MSDUK-Consensus - FFG_GZ_2h vs. WGS_IL_N_1

• FFPE-MSDUK-Consensus - FFG_GZ_6h vs. WGS_IL_N_1

• FFPE-MSDUK-Consensus - FFG_GZ_24h vs. WGS_IL_N_1

TNscope

• TNscope - FFX_IL_1h

• TNscope - FFX_IL_2h

• TNscope - FFX_IL_6h

• TNscope - FFX_IL_24h

• TNscope - FFX_GZ_1h

• TNscope - FFX_GZ_6h

• TNscope - FFX_GZ_24h

• TNscope - FFG_IL_1h

• TNscope - FFG_IL_2h

• TNscope - FFG_IL_6h

• TNscope - FFG_IL_24h

• TNscope - FFG_GZ_1h

• TNscope - FFG_GZ_2h

• TNscope - FFG_GZ_6h

• TNscope - FFG_GZ_24h

• Sentieon TNscope WF FFX_IL_T_1h_1_vs_WES_IL_N_1

• Sentieon TNscope WF FFX_IL_T_2h_1_vs_WES_IL_N_1

• Sentieon TNscope WF FFX_IL_T_6h_1_vs_WES_IL_N_1

• Sentieon TNscope WF FFX_IL_T_24h_1_vs_WES_IL_N_1

• Sentieon TNscope WF FFX_GZ_T_1h_1_vs_WES_IL_N_1

• Sentieon TNscope WF FFX_GZ_T_6h_3_vs_WES_IL_N_1

• Sentieon TNscope WF FFX_GZ_T_24h_1_vs_WES_IL_N_1

• TNscope - FFG_IL_1h vs WGS_IL_N_1

• TNscope - FFG_IL_2h vs WGS_IL_N_1

• TNscope - FFG_IL_6h vs WGS_IL_N_1

• TNscope - FFG_IL_24h vs WGS_IL_N_1

• TNscope - FFG_GZ_1h vs WGS_IL_N_1

• TNscope - FFG_GZ_2h_vs_WGS_IL_N_1

• TNscope - FFG_GZ_6h vs WGS_IL_N_1

• TNscope - FFG_GZ_24h vs WGS_IL_N_1