Sequencing

File naming convention below:

Data availability

All the raw sequencing data have been deposited to NCBI's SRA (SRP162370).

Some BAM files aligned with BWA MEM can also be obtained on NCBI's FTP site.

Whole Genome Sequencing for Reference Samples on Illumina Platforms

Somatic mutation callers were run with the following 21 pairings (each was aligned with three different aligners to create a total of 63 tumor-normal BAM files here).

• HiSeq at Illumina

  • WGS_IL_T_1 vs. WGS_IL_N_1

  • WGS_IL_T_2 vs. WGS_IL_N_2

  • WGS_IL_T_3 vs. WGS_IL_N_3

• NovaSeq at Illumina

  • WGS_NS_T_1 vs. WGS_NS_N_1

  • WGS_NS_T_2 vs. WGS_NS_N_2

  • WGS_NS_T_3 vs. WGS_NS_N_3

  • WGS_NS_T_4 vs. WGS_NS_N_4

  • WGS_NS_T_5 vs. WGS_NS_N_5

  • WGS_NS_T_6 vs. WGS_NS_N_6

  • WGS_NS_T_7 vs. WGS_NS_N_7

  • WGS_NS_T_8 vs. WGS_NS_N_8

  • WGS_NS_T_9 vs. WGS_NS_N_9

• HiSeq at Fudan University

  • WGS_FD_T_1 vs. WGS_FD_N_1

  • WGS_FD_T_2 vs. WGS_FD_N_2

  • WGS_FD_T_3 vs. WGS_FD_N_3

• HiSeq at Novartis

  • WGS_NV_T_1 vs. WGS_NV_N_1

  • WGS_NV_T_2 vs. WGS_NV_N_2

  • WGS_NV_T_3 vs. WGS_NV_N_3

• HiSeq at National Cancer Institute

  • WGS_NC_T_1 vs. WGS_NC_N_1

• Loma Linda University

  • WGS_LL_T_1 vs. WGS_LL_N_1

• European Infrastructure for Translational Medicine (EATRIS)

  • WGS_EA_T_1 vs. WGS_EA_N_1

Tumor Purity Titration on Illumina HiSeq Platform

Three replicates were also combined to make 350X data sets.

• HiSeq at Genentech ( Tumor-Normal Ratio, _Replicate# )

  • SPP_GT_1-0_1, SPP_GT_1-0_2, SPP_GT_1-0_3

  • SPP_GT_3-1_1, SPP_GT_3-1_2, SPP_GT_3-1_3,

  • SPP_GT_1-1_1, SPP_GT_1-1_2, SPP_GT_1-1_3

  • SPP_GT_1-4_1, SPP_GT_1-4_2, SPP_GT_1-4_3,

  • SPP_GT_1-9_1, SPP_GT_1-9_2, SPP_GT_1-9_3,

  • SPP_GT_1-19_1, SPP_GT_1-19_2, SPP_GT_1-19_3,

  • SPP_GT_0-1_1, SPP_GT_0-1_2, SPP_GT_0-1_3

SPP_GT_1-0_1, SPP_GT_1-0_2, and SPP_GT_1-0_3 were combined into a 350X tumor sequencing data set.

SPP_GT_0-1_1, SPP_GT_0-1_2, and SPP_GT_0-1_3 were combined into a 350X normal sequencing data set.

PacBio Sequel Platform WGS

• • PBO_WC_T_1 vs. PBO_WC_N_1

Targeted Sequencing

AmpliSeq on Illumina MiSeq

• Tumor: AMS_AB_T_1, AMS_AB_T_2, AMS_AB_T_3

• Normal: AMS_AB_N_1, AMS_AB_N_2, AMS_AB_N_3

Whole Exome Sequencing

Illumina Sequencers

• • WES_IL_T_1 vs. WES_IL_N_1

  • WES_IL_T_2 vs. WES_IL_N_2

  • WES_IL_T_3 vs. WES_IL_N_3

  • WES_FD_T_1 vs. WES_FD_N_1

  • WES_FD_T_2 vs. WES_FD_N_2

  • WES_FD_T_3 vs. WES_FD_N_3

  • WES_NV_T_1 vs. WES_NV_N_1

  • WES_NV_T_2 vs. WES_NV_N_2

  • WES_NV_T_3 vs. WES_NV_N_3

  • WES_LL_T_1 vs. WES_LL_N_1

  • WES_NC_T_1 vs. WES_NC_N_1

  • WES_EA_T_1 vs. WES_EA_N_1

Ion Torrent Ion S5 Sequencer

• • INT_EA_T_1 vs. INT_EA_N_1

Different Library Preps and DNA input amounts on Illumina Platform

• • LBP_LL_T_1ng vs. LBP_LL_N_1ng

  • LBP_LL_T_10ng vs. LBP_LL_N_10ng

  • LBP_LL_T_100ng vs. LBP_LL_N_100ng

  • LBP_LL_T_250ng vs. LBP_LL_N_250ng

  • LBP_HS_T_1ng_1 vs. LBP_HS_N_1ng_1

  • LBP_HS_T_10ng_1 vs. LBP_HS_N_10ng_1

  • LBP_HS_N_100ng_1 vs. LBP_HS_T_100ng_1

FFPE on Illumina Platform

Whole genome sequencing

• • FFG_IL_N_1h, FFG_IL_T_1h

  • FFG_IL_N_2h, FFG_IL_T_2h

  • FFG_IL_N_6h, FFG_IL_T_6h

  • FFG_IL_N_24h, FFG_IL_T_24h

  • FFG_GZ_N_1h-B, FFG_GZ_N_1h-F, FFG_GZ_T_1h-A, FFG_GZ_T_1h-B, FFG_GZ_T_1h-E

  • FFG_GZ_N_2h-A, FFG_GZ_N_2h-E, FFG_GZ_T_2h-A, FFG_GZ_T_2h-B

  • FFG_GZ_N_6h-A, FFG_GZ_N_6h-E, FFG_GZ_T_6h-A, FFG_GZ_T_6h-B

  • FFG_GZ_N_24h-B, FFG_GZ_N_24h-C, FFG_GZ_N_24h-F, FFG_GZ_T_24h-B, FFG_GZ_T_24h-F

Whole exome sequencing

• • FFX_IL_N_1h_2, FFX_IL_T_1h_1

  • FFX_IL_N_2h_2, FFX_IL_T_2h_1

  • FFX_IL_N_6h_2, FFX_IL_T_6h_1

  • FFX_IL_N_24h_2, FFX_IL_T_24h_1

  • FFX_GZ_N_1h_1, FFX_GZ_T_1h_1, FFX_GZ_T_1h_3

  • FFX_GZ_N_2h_3

  • FFX_GZ_N_6h_1, FFX_GZ_T_6h_3

  • FFX_GZ_N_24h_1, FFX_GZ_T_24h_1, FFX_GZ_T_24h_2

10X Chromium Linked Reads Platform

• • CHR_EA_N_1, CHR_EA_T_1

  • CHR_NC_N_1, CHR_NC_T_1

  • CHR_FD_N_1, CHR_FD_N_2, CHR_FD_N_3, CHR_FD_T_1, CHR_FD_T_2, CHR_FD_T_3

  • CHR_IL_N_1, CHR_IL_N_2, CHR_IL_N_3, CHR_IL_T_1, CHR_IL_T_2, CHR_IL_T_3

  • CHR_NV_N_1, CHR_NV_N_2, CHR_NV_N_3, CHR_NV_T_1, CHR_NV_T_2, CHR_NV_T_3