Data and jobs on Seven Bridge Genomics

somaticCaller code:

• MuTect2 (M), SomaticSniper (S), VarDict (D), MuSE (U), Strelka (K), TNscope (T)

• VarDict seems to have problem with SOAP-generated BAM files. A miniTest has 8 simultaneous thread on a pair of mini BAM for over an hour, and none has finished.

Somatic Mutation Output from 21 WGS Replicates (63 pair of BAM files)

IL_T_1 vs. IL_N_1:

• BWA

  • CallableLoci complete: gatk callableloci job ($1.43)

  • MuTect2 complete: mutect2-workflow job ($5.81) and mutect2 vcf file.

  • SomaticSniper complete: somaticsniper job ($1.68) and somaticsniper vcf file.

  • VarDict complete: vardict-workflow job ($4.17). Needed to sort the vcf file. This is the sorted vardict vcf file.

  • MuSE complete: parallel-muse-workflow job ($5.60) and muse vcf file.

  • Strelka complete: parallel-strelka-workflow job ($1.89). Needed to sort the two vcf files: snv and indel. These are the sorted strelka snv and indel vcf files.

  • SomaticSeq complete (fallback mode, no machine learning): single threaded somaticseq job ($3.99)

    • consensus vcf files: snv, indel

    • tsv files: snv, indel

  • Output files copied to SNV project:

    • CallableLoci, CallableLoci Summary, MuTect2, SomaticSniper, VarDict, MuSE, Strelka SNV, Strelka INDEL, SomaticSeq SNV TSV, SomaticSeq INDEL TSV, SomaticSeq Consensus SNV VCF, SomaticSeq Consensus INDEL VCF

• Novoalign

  • CallableLoci complete: gatk callableloci job ($1.40)

  • MuTect2 complete: parallel-mutect2-workflow job ($7.44) and mutect2 vcf file.

  • SomaticSniper complete: somaticsniper job ($1.63) and somaticsniper vcf file.

  • VarDict complete: parallel-vardict-workflow job ($4.21) and vardict vcf file.

  • MuSE complete: parallel-muse-workflow job ($5.59) and muse vcf file.

  • Strelka complete: parallel-strelka-workflow job ($1.78) and strelka's snv and indel vcf file

  • SomaticSeq complete (fallback mode, no machine learning): single-threaded somaticseq job ($3.24)

    • consensus vcf files: snv, indel

    • tsv files: snv, indel

  • Output files copied to SNV project:

    • CallableLoci, Callable Summary, MuTect2, SomaticSniper, VarDict, MuSE, Strelka SNV, Strelka INDEL, SomaticSeq SNV TSV, SomaticSeq INDEL TSV, SomaticSeq Consensus SNV VCF, SomaticSeq Consensus INDEL VCF

• Bowtie2

  • CallableLoci complete: gatk callableloci job ($1.42)

  • somaticCallers-MSDUK (MuTect2/SomaticSniper/VarDict/MuSE/Strelka) complete: somaticCallers-MSDUK job ($21.07)

    • job output: mutect2 vcf file, somaticsniper vcf file (missing header), vardict vcf file, muse vcf file, strelka snv vcf file, strelka indel vcf file

    • somaticsniper vcf file with header added back

  • SomaticSeq job (consensus mode, no machine learning) complete: workflow job

  • Output files copied to SNV project:

    • CallableLoci, Callable Summary, MuTect2, SomaticSniper, VarDict, MuSE, Strelka SNV, Strelka INDEL, SomaticSeq SNV TSV, SomaticSeq INDEL TSV, SomaticSeq Consensus SNV VCF, SomaticSeq Consensus INDEL VCF

• SOAP

  • CallableLoci complete: gatk callableloci job ($1.44)

  • somaticCallers-MSUK (MuTect2/SomaticSniper/MuSE/Strelka) complete: somaticCallers-MSUK job

    • job output: mutect2 vcf file, somaticsniper vcf file (lost the header), muse vcf file, strelka snv vcf file, strelka indel vcf file

    • somaticsniper vcf file with header added back

  • Output files copied to SNV project:

    • CallableLoci, Callable Summary, MuTect2, SomaticSniper, MuSE, Strelka SNV, Strelka INDEL

IL_T_2 vs. IL_N_2:

• BWA

  • CallableLoci job complete: https://cgc.sbgenomics.com/u/xiaowen/fda-seqc2-wg-1/tasks/12f6e58a-15a8-4a67-8c3e-93ac41b87917/

  • parallel-somaticseq-workflow-MSDUK complete: workflow job

  • parallel-scalpel-workflow submitted: https://cgc.sbgenomics.com/u/xiaowen/fda-seqc2-wg-1/tasks/ce14b693-f4bf-4bd8-946a-d9ce86f6998d

  • Output files copied to SNV projects:

    • CallableLoci, Callable Summary, MuTect2, SomaticSniper, VarDict, MuSE, Strelka SNV, Strelka INDEL, SomaticSeq SNV TSV, SomaticSeq INDEL TSV, SomaticSeq Consensus SNV VCF, SomaticSeq Consensus INDEL VCF

• Novoalign

  • parallel-somaticseq-workflow-MSDUK complete: workflow job

  • Output files copied to SNV project:

    • MuTect2, SomaticSniper, MuSE, VarDict, Strelka SNV, Strelka INDEL, SomaticSeq SNV TSV, SomaticSeq INDEL TSV, SomaticSeq Consensus SNV VCF, SomaticSeq Consensus INDEL VCF

• Bowtie2

  • parallel-somaticseq-workflow-MSDUK complete: workflow job

  • Output files copied to SNV project:

    • MuTect2, SomaticSniper, VarDict, MuSE, Strelka SNV, Strelka INDEL, SomaticSeq SNV TSV, SomaticSeq INDEL TSV, SomaticSeq Consensus SNV VCF, SomaticSeq Consensus INDEL VCF

IL_T_3 vs. IL_N_3

• CallableLoci: https://cgc.sbgenomics.com/u/xiaowen/fda-seqc2-wg-1/tasks/0da47426-9aeb-466b-a426-71f7c7ef266b

• BWA

  • parallel-somaticseq-workflow complete: workflow job

  • Output files copied to SNV project:

    • MuTect2, SomaticSniper, VarDict, MuSE, Strelka SNV, Strelka INDEL, SomaticSeq SNV TSV, SomaticSeq INDEL TSV, SomaticSeq Consensus SNV VCF, SomaticSeq Consensus INDEL VCF

• Novoalign

  • parallel-somaticseq-workflow complete: workflow job

  • Output files copied to SNV project:

    • MuTect2, SomaticSniper, VarDict, MuSE, Strelka SNV, Strelka INDEL, SomaticSeq SNV TSV, SomaticSeq INDEL TSV, SomaticSeq Consensus SNV VCF, SomaticSeq Consensus INDEL VCF

• Bowtie:

  • parallel-somaticseq-workflow complete: workflow job

  • Output files copied to SNV project:

    • MuTect2, SomaticSniper, VarDict, MuSE, Strelka SNV, Strelka INDEL, SomaticSeq SNV TSV, SomaticSeq INDEL TSV, SomaticSeq Consensus SNV VCF, SomaticSeq Consensus INDEL VCF

NS_T_1 vs. NS_N_1:

• BWA

  • CallableLoci for each aligner complete: callableloci_4x job

  • parallel-somaticseq-workflow-MSDUK complete: workflow job

  • Output files copied to SNV project:

    • CallableLoci, Callable Summary, MuTect2, SomaticSniper, VarDict, MuSE, Strelka SNV, Strelka INDEL, SomaticSeq SNV TSV, SomaticSeq INDEL TSV, SomaticSeq Consensus SNV VCF, SomaticSeq Consensus INDEL VCF

• Novoalign

  • parallel-somaticseq-workflow-MSDUK submitted: workflow job

  • Output files copied to SNV project:

    • CallableLoci, Callable Summary, MuTect2, SomaticSniper, VarDict, MuSE, Strelka SNV, Strelka INDEL, SomaticSeq SNV TSV, SomaticSeq INDEL TSV, SomaticSeq Consensus SNV VCF, SomaticSeq Consensus INDEL VCF

• Bowtie2

  • parallel-somaticseq-workflow-MSDUK complete: workflow job

  • Output files copied to SNV project:

    • CallableLoci, Callable Summary, MuTect2, SomaticSniper, VarDict, MuSE, Strelka SNV, Strelka INDEL, SomaticSeq SNV TSV, SomaticSeq INDEL TSV, SomaticSeq Consensus SNV VCF, SomaticSeq Consensus INDEL VCF

NS_T_2 vs. NS_N_2:

• BWA

  • CallableLoci for each aligner submitted: callableloci_4x job

  • parallel-somaticseq-workflow-MSDUK:

    • This is a failed job due to VarDict spitting out non-GCGAN character in VCF file.

    • Resubmitted with SomaticSeq v2.7.0 complete: workflow job

  • Output files copied to SNV project:

    • CallableLoci, Callable Summary, MuTect2, SomaticSniper, VarDict, MuSE, Strelka SNV, Strelka INDEL, SomaticSeq SNV TSV, SomaticSeq INDEL TSV, SomaticSeq Consensus SNV VCF, SomaticSeq Consensus INDEL VCF

• Novoalign

  • parallel-somaticseq-workflow-MSDUK complete: workflow job

  • Output files copied to SNV project:

    • CallableLoci, Callable Summary, MuTect2, SomaticSniper, VarDict, MuSE, Strelka SNV, Strelka INDEL, SomaticSeq SNV TSV, SomaticSeq INDEL TSV, SomaticSeq Consensus SNV VCF, SomaticSeq Consensus INDEL VCF

• Bowtie2

  • parallel-somaticseq-workflow-MSDUK complete: workflow job

  • Output files copied to SNV project:

    • CallableLoci, Callable Summary, MuTect2, SomaticSniper, VarDict, MuSE, Strelka SNV, Strelka INDEL, SomaticSeq SNV TSV, SomaticSeq INDEL TSV, SomaticSeq Consensus SNV VCF, SomaticSeq Consensus INDEL VCF

NS_T_3 vs. NS_N_3:

• BWA

  • CallableLoci for each aligner complete: callableloci_4x job

  • parallel-somaticseq-workflow-MSDUK complete: workflow job

  • Output files copied to SNV project:

    • CallableLoci, Callable Summary, MuTect2, SomaticSniper, VarDict, MuSE, Strelka SNV, Strelka INDEL, SomaticSeq SNV TSV, SomaticSeq INDEL TSV, SomaticSeq Consensus SNV VCF, SomaticSeq Consensus INDEL VCF

• Novoalign

  • parallel-somaticseq-workflow-MSDUK complete: workflow job

  • Output files copied to SNV project:

    • CallableLoci, Callable Summary, MuTect2, SomaticSniper, VarDict, MuSE, Strelka SNV, Strelka INDEL, SomaticSeq SNV TSV, SomaticSeq INDEL TSV, SomaticSeq Consensus SNV VCF, SomaticSeq Consensus INDEL VCF

• Bowtie2:

  • parallel-somaticseq-workflow-MSDUK complete: workflow job

  • Output files copied to SNV project:

    • CallableLoci, Callable Summary, MuTect2, SomaticSniper, VarDict, MuSE, Strelka SNV, Strelka INDEL, SomaticSeq SNV TSV, SomaticSeq INDEL TSV, SomaticSeq Consensus SNV VCF, SomaticSeq Consensus INDEL VCF

NS_T_4 vs. NS_N_4

• CallableLoci: https://cgc.sbgenomics.com/u/xiaowen/fda-seqc2-wg-1/tasks/18c68d84-c9d4-4770-95e0-f0c7458cd49b

• BWA

  • parallel-somaticseq-workflow complete: workflow job

  • Output files copied to SNV project:

    • MuTect2, SomaticSniper, VarDict, MuSE, Strelka SNV, Strelka INDEL, SomaticSeq SNV TSV, SomaticSeq INDEL TSV, SomaticSeq Consensus SNV VCF, SomaticSeq Consensus INDEL VCF

• Novoalign

  • parallel-somaticseq-workflow complete: workflow job

  • Output files copied to SNV project:

    • MuTect2, SomaticSniper, VarDict, MuSE, Strelka SNV, Strelka INDEL, SomaticSeq SNV TSV, SomaticSeq INDEL TSV, SomaticSeq Consensus SNV VCF, SomaticSeq Consensus INDEL VCF

• Bowtie

  • parallel-somaticseq-workflow complete: workflow job

  • Output files copied to SNV project:

    • MuTect2, SomaticSniper, VarDict, MuSE, Strelka SNV, Strelka INDEL, SomaticSeq SNV TSV, SomaticSeq INDEL TSV, SomaticSeq Consensus SNV VCF, SomaticSeq Consensus INDEL VCF

NS_T_5 vs. NS_N_5

• CallableLoci: https://cgc.sbgenomics.com/u/xiaowen/fda-seqc2-wg-1/tasks/b6bf96f8-e7d5-4adb-bce7-00b7272c9124

• BWA

  • parallel-somaticseq-workflow complete: workflow job

  • Output files copied to SNV project:

    • MuTect2, SomaticSniper, VarDict, MuSE, Strelka SNV, Strelka INDEL, SomaticSeq SNV TSV, SomaticSeq INDEL TSV, SomaticSeq Consensus SNV VCF, SomaticSeq Consensus INDEL VCF

• Novoalign

  • parallel-somaticseq-workflow complete: workflow job

  • Output files copied to SNV project:

    • MuTect2, SomaticSniper, VarDict, MuSE, Strelka SNV, Strelka INDEL, SomaticSeq SNV TSV, SomaticSeq INDEL TSV, SomaticSeq Consensus SNV VCF, SomaticSeq Consensus INDEL VCF

• Bowtie

  • parallel-somaticseq-workflow complete: workflow job

  • Output files copied to SNV project:

    • MuTect2, SomaticSniper, VarDict, MuSE, Strelka SNV, Strelka INDEL, SomaticSeq SNV TSV, SomaticSeq INDEL TSV, SomaticSeq Consensus SNV VCF, SomaticSeq Consensus INDEL VCF

NS_T_6 vs. NS_N_6

• CallableLoci: https://cgc.sbgenomics.com/u/xiaowen/fda-seqc2-wg-1/tasks/1df91346-82fd-4e70-bf3d-f2a2f9c4b111

• BWA

  • parallel-somaticseq-workflow complete: workflow job

  • Output files copied to SNV project:

    • MuTect2, SomaticSniper, VarDict, MuSE, Strelka SNV, Strelka INDEL, SomaticSeq SNV TSV, SomaticSeq INDEL TSV, SomaticSeq Consensus SNV VCF, SomaticSeq Consensus INDEL VCF

• Novoalign

  • parallel-somaticseq-workflow complete: workflow job (changed one file name)

  • Output files copied to SNV project:

    • MuTect2, SomaticSniper, VarDict, MuSE, Strelka SNV, Strelka INDEL, SomaticSeq SNV TSV, SomaticSeq INDEL TSV, SomaticSeq Consensus SNV VCF, SomaticSeq Consensus INDEL VCF

• Bowtie

  • parallel-somaticseq-workflow complete: workflow job

  • Output files copied to SNV project:

    • MuTect2, SomaticSniper, VarDict, MuSE, Strelka SNV, Strelka INDEL, SomaticSeq SNV TSV, SomaticSeq INDEL TSV, SomaticSeq Consensus SNV VCF, SomaticSeq Consensus INDEL VCF

NS_T_7 vs. NS_N_7

• CallableLoci: https://cgc.sbgenomics.com/u/xiaowen/fda-seqc2-wg-1/tasks/75e89540-8c8a-45ad-ba83-eb5ef23f2f9b

• BWA

  • parallel-somaticseq-workflow complete: workflow job

  • Output files copied to SNV project:

    • MuTect2, SomaticSniper, VarDict, MuSE, Strelka SNV, Strelka INDEL, SomaticSeq SNV TSV, SomaticSeq INDEL TSV, SomaticSeq Consensus SNV VCF, SomaticSeq Consensus INDEL VCF

• Novoalign

  • parallel-somaticseq-workflow complete: workflow job

  • Output files copied to SNV project:

    • MuTect2, SomaticSniper, VarDict, MuSE, Strelka SNV, Strelka INDEL, SomaticSeq SNV TSV, SomaticSeq INDEL TSV, SomaticSeq Consensus SNV VCF, SomaticSeq Consensus INDEL VCF

• Bowtie

  • parallel-somaticseq-workflow complete: workflow job

  • Output files copied to SNV project:

    • MuTect2, SomaticSniper, VarDict, MuSE, Strelka SNV, Strelka INDEL, SomaticSeq SNV TSV, SomaticSeq INDEL TSV, SomaticSeq Consensus SNV VCF, SomaticSeq Consensus INDEL VCF

NS_T_8 vs. NS_N_8

• CallableLoci: https://cgc.sbgenomics.com/u/xiaowen/fda-seqc2-wg-1/tasks/ee0d769c-f9e1-4af7-aba7-d4eab7215d3c

• BWA

  • parallel-somaticseq-workflow complete: workflow job (changed one file name)

  • Output files copied to SNV project:

    • MuTect2, SomaticSniper, VarDict, MuSE, Strelka SNV, Strelka INDEL, SomaticSeq SNV TSV, SomaticSeq INDEL TSV, SomaticSeq Consensus SNV VCF, SomaticSeq Consensus INDEL VCF

• Novoalign

  • parallel-somaticseq-workflow complete: workflow job

  • Output files copied to SNV project:

    • MuTect2, SomaticSniper, VarDict, MuSE, Strelka SNV, Strelka INDEL, SomaticSeq SNV TSV, SomaticSeq INDEL TSV, SomaticSeq Consensus SNV VCF, SomaticSeq Consensus INDEL VCF

• Bowtie

  • parallel-somaticseq-workflow complete: workflow job

  • Output files copied to SNV project:

    • MuTect2, SomaticSniper, VarDict, MuSE, Strelka SNV, Strelka INDEL, SomaticSeq SNV TSV, SomaticSeq INDEL TSV, SomaticSeq Consensus SNV VCF, SomaticSeq Consensus INDEL VCF

NS_T_9 vs. NS_N_9

• CallableLoci: https://cgc.sbgenomics.com/u/xiaowen/fda-seqc2-wg-1/tasks/015f1899-b583-4e16-bcaf-6703a2da938c

• BWA

  • parallel-somaticseq-workflow complete: workflow job

  • Output files copied to SNV project:

    • MuTect2, SomaticSniper, VarDict, MuSE, Strelka SNV, Strelka INDEL, SomaticSeq SNV TSV, SomaticSeq INDEL TSV, SomaticSeq Consensus SNV VCF, SomaticSeq Consensus INDEL VCF

• Novoalign:

  • parallel-somaticseq-workflow complete: workflow job

  • Output files copied to SNV project:

    • MuTect2, SomaticSniper, VarDict, MuSE, Strelka SNV, Strelka INDEL, SomaticSeq SNV TSV, SomaticSeq INDEL TSV, SomaticSeq Consensus SNV VCF, SomaticSeq Consensus INDEL VCF

• Bowtie

  • parallel-somaticseq-workflow complete: workflow job

  • Output files copied to SNV project:

    • MuTect2, SomaticSniper, VarDict, MuSE, Strelka SNV, Strelka INDEL, SomaticSeq SNV TSV, SomaticSeq INDEL TSV, SomaticSeq Consensus SNV VCF, SomaticSeq Consensus INDEL VCF

NV_T_1 vs. NV_N_1

• BWA

  • parallel-somaticseq-workflow complete: workflow job

  • Output files copied to SNV project:

    • MuTect2, SomaticSniper, VarDict, MuSE, Strelka SNV, Strelka INDEL, SomaticSeq SNV TSV, SomaticSeq INDEL TSV, SomaticSeq Consensus SNV VCF, SomaticSeq Consensus INDEL VCF

• Novoalign

  • parallel-somaticseq-workflow complete: workflow job

  • Output files copied to SNV project:

    • MuTect2, SomaticSniper, VarDict, MuSE, Strelka SNV, Strelka INDEL, SomaticSeq SNV TSV, SomaticSeq INDEL TSV, SomaticSeq Consensus SNV VCF, SomaticSeq Consensus INDEL VCF

• Bowtie

  • parallel-somaticseq-workflow complete: workflow job

  • Output files copied to SNV project:

    • MuTect2, SomaticSniper, VarDict, MuSE, Strelka SNV, Strelka INDEL, SomaticSeq SNV TSV, SomaticSeq INDEL TSV, SomaticSeq Consensus SNV VCF, SomaticSeq Consensus INDEL VCF

NV_T_2 vs. NV_N_2

• BWA

  • parallel-somaticseq-workflow complete: workflow job

  • Output files copied to SNV project:

    • MuTect2, SomaticSniper, VarDict, MuSE, Strelka SNV, Strelka INDEL, SomaticSeq SNV TSV, SomaticSeq INDEL TSV, SomaticSeq Consensus SNV VCF, SomaticSeq Consensus INDEL VCF

• Novoalign

  • parallel-somaticseq-workflow complete: workflow job

  • Output files copied to SNV project:

    • MuTect2, SomaticSniper, VarDict, MuSE, Strelka SNV, Strelka INDEL, SomaticSeq SNV TSV, SomaticSeq INDEL TSV, SomaticSeq Consensus SNV VCF, SomaticSeq Consensus INDEL VCF

• Bowtie

  • parallel-somaticseq-workflow complete: workflow job

  • Output files copied to SNV project:

    • MuTect2, SomaticSniper, VarDict, MuSE, Strelka SNV, Strelka INDEL, SomaticSeq SNV TSV, SomaticSeq INDEL TSV, SomaticSeq Consensus SNV VCF, SomaticSeq Consensus INDEL VCF

NV_T_3 vs. NV_N_3

• BWA

  • parallel-somaticseq-workflow complete: workflow job

  • Output files copied to SNV project:

    • MuTect2, SomaticSniper, VarDict, MuSE, Strelka SNV, Strelka INDEL, SomaticSeq SNV TSV, SomaticSeq INDEL TSV, SomaticSeq Consensus SNV VCF, SomaticSeq Consensus INDEL VCF

• Novoalign

  • parallel-somaticseq-workflow complete: workflow job

  • Output files copied to SNV project:

    • MuTect2, SomaticSniper, VarDict, MuSE, Strelka SNV, Strelka INDEL, SomaticSeq SNV TSV, SomaticSeq INDEL TSV, SomaticSeq Consensus SNV VCF, SomaticSeq Consensus INDEL VCF

• Bowtie2

  • parallel-somaticseq-workflow complete: workflow job

  • Output files copied to SNV project:

    • MuTect2, SomaticSniper, VarDict, MuSE, Strelka SNV, Strelka INDEL, SomaticSeq SNV TSV, SomaticSeq INDEL TSV, SomaticSeq Consensus SNV VCF, SomaticSeq Consensus INDEL VCF

FD_T_1 vs. FD_N_1

• BWA

  • parallel-somaticseq-workflow complete: workflow job

  • Output files copied to SNV project:

    • MuTect2, SomaticSniper, VarDict, MuSE, Strelka SNV, Strelka INDEL, SomaticSeq SNV TSV, SomaticSeq INDEL TSV, SomaticSeq Consensus SNV VCF, SomaticSeq Consensus INDEL VCF

  • An demonstration of SomaticSeq.Wrapper.sh with TNscope:

  • https://cgc.sbgenomics.com/u/xiaowen/fda-seqc2-wg-1/tasks/de34947e-6b6c-4796-8546-d7d2c71259ee/#

• Novoalign

  • parallel-somaticseq-workflow complete: workflow job

  • Output files copied to SNV project:

    • MuTect2, SomaticSniper, VarDict, MuSE, Strelka SNV, Strelka INDEL, SomaticSeq SNV TSV, SomaticSeq INDEL TSV, SomaticSeq Consensus SNV VCF, SomaticSeq Consensus INDEL VCF

• Bowtie2

  • parallel-somaticseq-workflow complete: workflow job

  • Output files copied to SNV project:

    • MuTect2, SomaticSniper, VarDict, MuSE, Strelka SNV, Strelka INDEL, SomaticSeq SNV TSV, SomaticSeq INDEL TSV, SomaticSeq Consensus SNV VCF, SomaticSeq Consensus INDEL VCF

FD_T_2 vs. FD_N_2

• BWA

  • parallel-somaticseq-workflow complete: workflow job

  • Output files copied to SNV project:

    • MuTect2, SomaticSniper, VarDict, MuSE, Strelka SNV, Strelka INDEL, SomaticSeq SNV TSV, SomaticSeq INDEL TSV, SomaticSeq Consensus SNV VCF, SomaticSeq Consensus INDEL VCF

• Novoalign

  • parallel-somaticseq-workflow complete: workflow job

  • Output files copied to SNV project:

    • MuTect2, SomaticSniper, VarDict, MuSE, Strelka SNV, Strelka INDEL, SomaticSeq SNV TSV, SomaticSeq INDEL TSV, SomaticSeq Consensus SNV VCF, SomaticSeq Consensus INDEL VCF

• Bowtie2

  • parallel-somaticseq-workflow complete: workflow job

  • Output files copied to SNV project:

    • MuTect2, SomaticSniper, VarDict, MuSE, Strelka SNV, Strelka INDEL, SomaticSeq SNV TSV, SomaticSeq INDEL TSV, SomaticSeq Consensus SNV VCF, SomaticSeq Consensus INDEL VCF

FD_T_3 vs. FD_N_3

• BWA

  • parallel-somaticseq-workflow complete: workflow job

  • Output files copied to SNV project:

    • MuTect2, SomaticSniper, VarDict, MuSE, Strelka SNV, Strelka INDEL, SomaticSeq SNV TSV, SomaticSeq INDEL TSV, SomaticSeq Consensus SNV VCF, SomaticSeq Consensus INDEL VCF

• Novoalign

  • parallel-somaticseq-workflow complete: workflow job

  • Output files copied to SNV project:

    • MuTect2, SomaticSniper, VarDict, MuSE, Strelka SNV, Strelka INDEL, SomaticSeq SNV TSV, SomaticSeq INDEL TSV, SomaticSeq Consensus SNV VCF, SomaticSeq Consensus INDEL VCF

• Bowtie2

  • parallel-somaticseq-workflow complete: workflow job

  • Output files copied to SNV project:

    • MuTect2, SomaticSniper, VarDict, MuSE, Strelka SNV, Strelka INDEL, SomaticSeq SNV TSV, SomaticSeq INDEL TSV, SomaticSeq Consensus SNV VCF, SomaticSeq Consensus INDEL VCF

EA_T_1 vs EA_N_1:

• BWA

  • CallableLoci for each aligner complete: callableloci_4x job

  • somaticCallers-MSDUK complete: workflow job ($19.58)

  • SomaticSeq complete: workflow job

  • Output files copied to SNV project:

    • CallableLoci, Callable Summary, MuTect2, SomaticSniper, VarDict, MuSE, Strelka SNV, Strelka INDEL, SomaticSeq SNV TSV, SomaticSeq INDEL TSV, SomaticSeq Consensus SNV VCF, SomaticSeq Consensus INDEL VCF

• Novoalign

  • somaticCallers-MSDUK complete: workflow job ($21.37)

  • SomaticSeq complete: workflow job

  • Output files copied to SNV project:

    • CallableLoci, Callable Summary, MuTect2, SomaticSniper, VarDict, MuSE, Strelka SNV, Strelka INDEL, SomaticSeq SNV TSV, SomaticSeq INDEL TSV, SomaticSeq Consensus SNV VCF, SomaticSeq Consensus INDEL VCF

    • 
      

• Bowtie2

  • somaticCallers-MSDUK complete: workflow job ($20.42)

  • SomaticSeq complete: somaticseq job

  • Output files copied to SNV project:

    • CallableLoci, Callable Summary, MuTect2, SomaticSniper, VarDict, MuSE, Strelka SNV, Strelka INDEL, SomaticSeq SNV TSV, SomaticSeq INDEL TSV, SomaticSeq Consensus SNV VCF, SomaticSeq Consensus INDEL VCF

• SOAP

  • somaticCallers-MSUK complete: workflow job ($19.57)

  • Output files copied to SNV project:

    • CallableLoci, Callable Summary, MuTect2, SomaticSniper, VarDict, MuSE, Strelka SNV, Strelka INDEL, SomaticSeq SNV TSV, SomaticSeq INDEL TSV, SomaticSeq Consensus SNV VCF, SomaticSeq Consensus INDEL VCF

NC_T_1 vs NC_N_1

• BWA

  • CallableLoci for each aligner submitted:

    • FAILED job. FAIL log indicate multiple SMs are present in the soap.bam's header.

    • Resubmit substitute the soap bam with bwa normal bam complete: callableloci_4x job

  • parallel-somaticseq-workflow-MSDUK complete: workflow job

  • Output files copied to SNV project:

    • CallableLoci, Callable Summary, MuTect2, SomaticSniper, VarDict, MuSE, Strelka SNV, Strelka INDEL, SomaticSeq SNV TSV, SomaticSeq INDEL TSV, SomaticSeq Consensus SNV VCF, SomaticSeq Consensus INDEL VCF

• Novoalign

  • parallel-somaticseq-workflow-MSDUK complete: workflow job

  • Output files copied to SNV project:

    • CallableLoci, Callable Summary, MuTect2, SomaticSniper, VarDict, MuSE, Strelka SNV, Strelka INDEL, SomaticSeq SNV TSV, SomaticSeq INDEL TSV, SomaticSeq Consensus SNV VCF, SomaticSeq Consensus INDEL VCF

• Bowtie2

  • parallel-somaticseq-workflow-MSDUK complete: workflow job

  • Output files copied to SNV project:

    • CallableLoci, Callable Summary, MuTect2, SomaticSniper, VarDict, MuSE, Strelka SNV, Strelka INDEL, SomaticSeq SNV TSV, SomaticSeq INDEL TSV, SomaticSeq Consensus SNV VCF, SomaticSeq Consensus INDEL VCF

LL_T_1 vs. LL_N_1

• BWA

  • parallel-somaticseq-workflow complete: workflow job

  • Output files copied to SNV project:

    • MuTect2, SomaticSniper, VarDict, MuSE, Strelka SNV, Strelka INDEL, SomaticSeq SNV TSV, SomaticSeq INDEL TSV, SomaticSeq Consensus SNV VCF, SomaticSeq Consensus INDEL VCF

• Novoalign

  • parallel-somaticseq-workflow complete: workflow job

  • Output files copied to SNV project:

    • MuTect2, SomaticSniper, VarDict, MuSE, Strelka SNV, Strelka INDEL, SomaticSeq SNV TSV, SomaticSeq INDEL TSV, SomaticSeq Consensus SNV VCF, SomaticSeq Consensus INDEL VCF

• Bowtie2

  • parallel-somaticseq-workflow complete: workflow job

  • Output files copied to SNV project:

    • MuTect2, SomaticSniper, VarDict, MuSE, Strelka SNV, Strelka INDEL, SomaticSeq SNV TSV, SomaticSeq INDEL TSV, SomaticSeq Consensus SNV VCF, SomaticSeq Consensus INDEL VCF

TNScope 201711.02:

• IL: https://cgc.sbgenomics.com/u/xiaowen/fda-seqc2-wg-1/tasks/88b24541-3771-4052-b2e1-3ad2fef34ad3/

• NS: https://cgc.sbgenomics.com/u/xiaowen/fda-seqc2-wg-1/tasks/f860d264-a608-473f-80f1-2aa8b15b8041/

• FD: https://cgc.sbgenomics.com/u/xiaowen/fda-seqc2-wg-1/tasks/21e80e20-e0dd-4f7f-b55f-2900931416fd/

• NV: https://cgc.sbgenomics.com/u/xiaowen/fda-seqc2-wg-1/tasks/d125f4b9-1398-4d15-ad5d-b7beec0eac4f/

• LL/EA/NC: https://cgc.sbgenomics.com/u/xiaowen/fda-seqc2-wg-1/tasks/c60f1780-bba2-4000-aa3c-a3407cdd7597/

A few of those runs above produced truncated VCF files, so their results are incomplete.

• WGS.novo.dedup-NV_T_3_vs_NV_N_3

The following 13 pairs were run as a batch job: Batch Job.

• WGS.bwa.dedup-EA_T_1_vs_EA_N_1

• WGS.novo.dedup-EA_T_1_vs_EA_N_1

• WGS.novo.dedup-FD_T_3_vs_FD_N_3

• WGS.bwa.dedup-NS_T_1_vs_NS_N_1

• WGS.bwa.dedup-NS_T_4_vs_NS_N_4

• WGS.bwa.dedup-NS_T_9_vs_NS_N_9

• WGS.novo.dedup-IL_T_2_vs_IL_N_2

• WGS.novo.dedup-IL_T_3_vs_IL_N_3

• WGS.novo.dedup-NS_T_3_vs_NS_N_3

• WGS.novo.dedup-NS_T_8_vs_NS_N_8

• WGS.novo.dedup-NC_T_1_vs_NC_N_1

• WGS.novo.dedup-NV_T_1_vs_NV_N_1

• WGS.novo.dedup-NV_T_2_vs_NV_N_2

The two Deep Sequencing WGS Data

Combined nine NovaSeq replicates and use one single "sample name" (380X)

Somatic Mutation Calling Results

• CombineNovaSeq.zip

BWA

• singleSM.WGS_NS_T_combine9.bwa.dedup.bam

• singleSM.WGS_NS_N_combine9.bwa.dedup.bam

• Somatic Mutation Calling

  • TNscope: TNscope 201711.02 - Combine 9 NovaSeq BWA (Rerun)

Bowtie

• singleSM.WGS_NS_T_combine9.bowtie.dedup.bam

• singleSM.WGS_NS_N_combine9.bowtie.dedup.bam

• Somatic Mutation Calling

  • TNscope: TNscope 201711.02 - Combine 9 NovaSeq Bowtie

NovoAlign

• singleSM.WGS_NS_T_combine9.novo.dedup.bam

• singleSM.WGS_NS_N_combine9.novo.dedup.bam

• Somatic Mutation Calling

  • TNscope: TNscope 201711.02 - Combine 9 NovaSeq NovoAlign (Rerun)

Use the Genentech 300X SPP with single "sample name" (300X)

Somatic Mutation Calling Results

• SPP.300X.zip

BWA

• Genentech.300X.Tumor.bwa.dedup.bam

• Genentech.300X.Normal.bwa.dedup.bam

Bowtie

• Genentech.300X.Tumor.bowtie.dedup.bam

• Genentech.300X.Normal.bowtie.dedup.bam

NovoAlign

• Genentech.300X.Tumor.novo.dedup.bam

• Genentech.300X.Normal.novo.dedup.bam

In silico mutation spike-in using BamSurgeon pipeline

Dockerized bamSurgeon pipeline available on SomaticSeq repo

• WGS_IL_N_1.bwa.dedup.bam

  • BAM: https://cgc.sbgenomics.com/u/xiaowen/fda-seqc2-wg-1/files/5a5941db4f0c428b3e113e9d/

  • SNV spiked in: https://cgc.sbgenomics.com/u/xiaowen/fda-seqc2-wg-1/files/5a5c04b14f0c428b3e117e8e/

  • INDEL spiked in: https://cgc.sbgenomics.com/u/xiaowen/fda-seqc2-wg-1/files/5a5c04ad4f0c428b3e117e89/

• WGS_IL_N_2.bwa.dedup.bam

  • BAM: https://cgc.sbgenomics.com/u/xiaowen/fda-seqc2-wg-1/files/5a5940d44f0c428b3e113e95/

  • SNV spiked in: https://cgc.sbgenomics.com/u/xiaowen/fda-seqc2-wg-1/files/5a5c04a94f0c428b3e117e83/

  • INDEL spiked in: https://cgc.sbgenomics.com/u/xiaowen/fda-seqc2-wg-1/files/5a5c04a64f0c428b3e117e7f/

• WGS_NS_N_1.bwa.dedup.bam

  • BAM: https://cgc.sbgenomics.com/u/xiaowen/fda-seqc2-wg-1/files/5a59443d4f0c428b3e113ead/

  • SNV spiked in: https://cgc.sbgenomics.com/u/xiaowen/fda-seqc2-wg-1/files/5a5c04c04f0c428b3e117ea7/

  • INDEL spiked in: https://cgc.sbgenomics.com/u/xiaowen/fda-seqc2-wg-1/files/5a5c04bd4f0c428b3e117ea1/

• WGS_NS_N_2.bwa.dedup.bam

  • BAM: https://cgc.sbgenomics.com/u/xiaowen/fda-seqc2-wg-1/files/5a5943114f0c428b3e113ea3/

  • SNV spiked in: https://cgc.sbgenomics.com/u/xiaowen/fda-seqc2-wg-1/files/5a5c04b84f0c428b3e117e9b/

  • INDEL spiked in: https://cgc.sbgenomics.com/u/xiaowen/fda-seqc2-wg-1/files/5a5c04b54f0c428b3e117e95/

• WGS_FD_N_2.bwa.dedup.bam

  • BAM: https://cgc.sbgenomics.com/u/xiaowen/fda-seqc2-wg-1/files/5a795b044f0c4abaed5ac39d/

  • SNV spiked in: https://cgc.sbgenomics.com/u/xiaowen/fda-seqc2-wg-1/files/5af4b2448950f600430151e3/

  • INDEL spike in: https://cgc.sbgenomics.com/u/xiaowen/fda-seqc2-wg-1/files/5af4b2418950f600430151d9/

• WGS_FD_N_3.bwa.dedup.bam

  • BAM: https://cgc.sbgenomics.com/u/xiaowen/fda-seqc2-wg-1/files/5a795bbd4f0c4abaed5ac3a0/

  • SNV spike in: https://cgc.sbgenomics.com/u/xiaowen/fda-seqc2-wg-1/files/5af4b24b8950f60043015237/

  • INDEL spiked in: https://cgc.sbgenomics.com/u/xiaowen/fda-seqc2-wg-1/files/5af4b2488950f60043015230/

• WGS_NV_N_2.bwa.dedup.bam

  • BAM: https://cgc.sbgenomics.com/u/xiaowen/fda-seqc2-wg-1/files/5a795c6b4f0c4abaed5ac3a3/

  • SNV spiked in: https://cgc.sbgenomics.com/u/xiaowen/fda-seqc2-wg-1/files/5af4b2528950f60043015245/

  • INDEL spiked in: https://cgc.sbgenomics.com/u/xiaowen/fda-seqc2-wg-1/files/5af4b24f8950f6004301523e/

• WGS_NV_N_3.bwa.dedup.bam

  • BAM: https://cgc.sbgenomics.com/u/xiaowen/fda-seqc2-wg-1/files/5a795dc94f0c4abaed5ac3a6/

  • SNV spiked in: https://cgc.sbgenomics.com/u/xiaowen/fda-seqc2-wg-1/files/5af4b25a8950f60043015253/

  • INDEL spiked in: https://cgc.sbgenomics.com/u/xiaowen/fda-seqc2-wg-1/files/5af4b2578950f6004301524c/

• WGS_IL_N_1.bowtie.dedup.bam

  • BAM: https://cgc.sbgenomics.com/u/xiaowen/fda-seqc2-wg-1/files/5a593dbf4f0c428b3e113e77/

  • SNV spiked in: https://cgc.sbgenomics.com/u/xiaowen/fda-seqc2-wg-1/files/5a5c04924f0c428b3e117e64/

  • INDEL spiked in: https://cgc.sbgenomics.com/u/xiaowen/fda-seqc2-wg-1/files/5a5c048e4f0c428b3e117e5f/

• WGS_IL_N_2.bowtie.dedup.bam

  • BAM: https://cgc.sbgenomics.com/u/xiaowen/fda-seqc2-wg-1/files/5a593aef4f0c428b3e113e71/

  • SNV spiked in: https://cgc.sbgenomics.com/u/xiaowen/fda-seqc2-wg-1/files/5a5c04864f0c428b3e117e56/

  • INDEL spiked in: https://cgc.sbgenomics.com/u/xiaowen/fda-seqc2-wg-1/files/5a5c04814f0c428b3e117e4d/

• WGS_NS_N_1.bowtie.dedup.bam

  • BAM: https://cgc.sbgenomics.com/u/xiaowen/fda-seqc2-wg-1/files/5a593ff84f0c428b3e113e8d/

  • SNV spiked in: https://cgc.sbgenomics.com/u/xiaowen/fda-seqc2-wg-1/files/5a5c04a24f0c428b3e117e77/

  • INDEL spiked in: https://cgc.sbgenomics.com/u/xiaowen/fda-seqc2-wg-1/files/5a5c049e4f0c428b3e117e71/

• WGS_NS_N_2.bowtie.dedup.bam

  • BAM: https://cgc.sbgenomics.com/u/xiaowen/fda-seqc2-wg-1/files/5a593f5b4f0c428b3e113e7f/

  • SNV spiked in: https://cgc.sbgenomics.com/u/xiaowen/fda-seqc2-wg-1/files/5a5c049a4f0c428b3e117e6e/

  • INDEL spiked in: https://cgc.sbgenomics.com/u/xiaowen/fda-seqc2-wg-1/files/5a5c04974f0c428b3e117e68/

• WGS_FD_N_2.bowtie.dedup.bam

  • BAM: https://cgc.sbgenomics.com/u/xiaowen/fda-seqc2-wg-1/files/5a7954874f0c4abaed5ac36d/

  • SNV spiked in: https://cgc.sbgenomics.com/u/xiaowen/fda-seqc2-wg-1/files/5af4b2258950f600430151a5/

  • INDEL spiked in: https://cgc.sbgenomics.com/u/xiaowen/fda-seqc2-wg-1/files/5af4b2218950f6004301519e/

• WGS_FD_N_3.bowtie.dedup.bam

  • BAM: https://cgc.sbgenomics.com/u/xiaowen/fda-seqc2-wg-1/files/5a79571f4f0c4abaed5ac394/

  • SNV spiked in: https://cgc.sbgenomics.com/u/xiaowen/fda-seqc2-wg-1/files/5af4b22c8950f600430151b3/

  • INDEL spiked in: https://cgc.sbgenomics.com/u/xiaowen/fda-seqc2-wg-1/files/5af4b2298950f600430151ac/

• WGS_NV_N_2.bowtie.dedup.bam

  • BAM: https://cgc.sbgenomics.com/u/xiaowen/fda-seqc2-wg-1/files/5a7958124f0c4abaed5ac397/

  • SNV spiked in: https://cgc.sbgenomics.com/u/xiaowen/fda-seqc2-wg-1/files/5af4b2348950f600430151c1/

  • INDEL spiked in: https://cgc.sbgenomics.com/u/xiaowen/fda-seqc2-wg-1/files/5af4b2318950f600430151ba/ 

• WGS_NV_N_3.bowtie.dedup.bam

  • BAM: https://cgc.sbgenomics.com/u/xiaowen/fda-seqc2-wg-1/files/5a7959734f0c4abaed5ac39a/

  • SNV spiked in: https://cgc.sbgenomics.com/u/xiaowen/fda-seqc2-wg-1/files/5af4b23d8950f600430151d2/

  • INDEL spiked in: https://cgc.sbgenomics.com/u/xiaowen/fda-seqc2-wg-1/files/5af4b2398950f600430151cb/

• WGS_IL_N_1.novo.dedup.bam

  • BAM: https://cgc.sbgenomics.com/u/xiaowen/fda-seqc2-wg-1/files/5a59463c4f0c428b3e113ebd/

  • SNV spiked in: https://cgc.sbgenomics.com/u/xiaowen/fda-seqc2-wg-1/files/5a5c04cd4f0c428b3e117ebc/

  • INDEL spiked in: https://cgc.sbgenomics.com/u/xiaowen/fda-seqc2-wg-1/files/5a5c04ca4f0c428b3e117eb9/

• WGS_IL_N_2.novo.dedup.bam

  • BAM: https://cgc.sbgenomics.com/u/xiaowen/fda-seqc2-wg-1/files/5a5944fb4f0c428b3e113eb5/

  • SNV spiked in: https://cgc.sbgenomics.com/u/xiaowen/fda-seqc2-wg-1/files/5a5c04c74f0c428b3e117eb3/

  • INDEL spiked in: https://cgc.sbgenomics.com/u/xiaowen/fda-seqc2-wg-1/files/5a5c04c34f0c428b3e117ead/

• WGS_NS_N_1.novo.dedup.bam

  • BAM: https://cgc.sbgenomics.com/u/xiaowen/fda-seqc2-wg-1/files/5a5948534f0c428b3e113ece/

  • SNV spiked in: https://cgc.sbgenomics.com/u/xiaowen/fda-seqc2-wg-1/files/5a5c04dc4f0c428b3e117ed4/

  • INDEL spiked in: https://cgc.sbgenomics.com/u/xiaowen/fda-seqc2-wg-1/files/5a5c04d94f0c428b3e117ed0/

• WGS_NS_N_2.novo.dedup.bam

  • BAM: https://cgc.sbgenomics.com/u/xiaowen/fda-seqc2-wg-1/files/5a5947854f0c428b3e113ec3/

  • SNV spiked in: https://cgc.sbgenomics.com/u/xiaowen/fda-seqc2-wg-1/files/5a5c04d44f0c428b3e117ec8/

  • INDEL spiked in: https://cgc.sbgenomics.com/u/xiaowen/fda-seqc2-wg-1/files/5a5c04d14f0c428b3e117ec2/

• WGS_FD_N_2.novo.dedup.bam

  • BAM: https://cgc.sbgenomics.com/u/xiaowen/fda-seqc2-wg-1/files/5a795f504f0c4abaed5ac3a9/

  • SNV spiked in: https://cgc.sbgenomics.com/u/xiaowen/fda-seqc2-wg-1/files/5af4b2628950f600430152b8/

  • INDEL spiked in: https://cgc.sbgenomics.com/u/xiaowen/fda-seqc2-wg-1/files/5af4b25e8950f6004301525d/

• WGS_FD_N_3.novo.dedup.bam

  • BAM: https://cgc.sbgenomics.com/u/xiaowen/fda-seqc2-wg-1/files/5a7960914f0c4abaed5ac3ac/

  • SNV spiked in: https://cgc.sbgenomics.com/u/xiaowen/fda-seqc2-wg-1/files/5af4b2688950f600430152c6/

  • INDEL spiked in: https://cgc.sbgenomics.com/u/xiaowen/fda-seqc2-wg-1/files/5af4b2658950f600430152bf/

• WGS_NV_N_2.novo.dedup.bam

  • BAM: https://cgc.sbgenomics.com/u/xiaowen/fda-seqc2-wg-1/files/5a7961694f0c4abaed5ac3af/

  • SNV spiked in: https://cgc.sbgenomics.com/u/xiaowen/fda-seqc2-wg-1/files/5af4b26f8950f6004301532a/

  • INDEL spiked in: https://cgc.sbgenomics.com/u/xiaowen/fda-seqc2-wg-1/files/5af4b26c8950f60043015323/

• WGS_NV_N_3.novo.dedup.bam

  • BAM: https://cgc.sbgenomics.com/u/xiaowen/fda-seqc2-wg-1/files/5a7963124f0c4abaed5ac3b2/

  • SNV spiked in: https://cgc.sbgenomics.com/u/xiaowen/fda-seqc2-wg-1/files/5af4b2768950f60043015338/

  • INDEL spiked in: https://cgc.sbgenomics.com/u/xiaowen/fda-seqc2-wg-1/files/5af4b2738950f60043015331/

In silico spike in for the two Deep Sequencing Data Sets

NovaSeq

Combine replicates 1-4 as normal, and use combined 5-9 for spike in

TNscope results from this group should be renamed with file extension of .vcf.gz. 

• BWA

  • singleSM.WGS_NS_N_combine1-4.bwa.dedup.bam

  • WGS_NS_1-4N_vs_5-9T.bwa.syntheticTumor.bam

  • WGS_NS_1-4N_vs_5-9T.bwa.synthetic_snvs.vcf

  • WGS_NS_1-4N_vs_5-9T.bwa.synthetic_indels.leftAlign.vcf

  • TNscope: TNscope 201711.02 - WGS_NS_1-4N_vs_5-9T.bwa

• Bowtie

  • singleSM.WGS_NS_N_combine1-4.bowtie.dedup.bam

  • WGS_NS_1-4N_vs_5-9T.bowtie.syntheticTumor.bam

  • WGS_NS_1-4N_vs_5-9T.bowtie.synthetic_snvs.vcf

  • WGS_NS_1-4N_vs_5-9T.bowtie.synthetic_indels.leftAlign.vcf

  • TNscope: TNscope 201711.02 - WGS_NS_1-4N_vs_5-9T.bowtie

• NovoAlign

  • singleSM.WGS_NS_N_combine1-4.novo.dedup.bam

  • WGS_NS_1-4N_vs_5-9T.novo.syntheticTumor.bam

  • WGS_NS_1-4N_vs_5-9T.novo.synthetic_snvs.vcf

  • WGS_NS_1-4N_vs_5-9T.novo.synthetic_indels.leftAlign.vcf

  • TNscope: TNscope 201711.02 - WGS_NS_1-4N_vs_5-9T.novo

Combine replicates 6-9 as normal, and use combined 1-5 for spike in

• BWA

  • singleSM.WGS_NS_N_combine6-9.bwa.dedup.bam

  • WGS_NS_6-9N_vs_1-5T.bwa.syntheticTumor.bam

  • WGS_NS_6-9N_vs_1-5T.bwa.synthetic_snvs.vcf

  • WGS_NS_6-9N_vs_1-5T.bwa.synthetic_indels.leftAlign.vcf

  • TNscope: TNscope 201711.02 - WGS_NS_6-9N_vs_1-5T.bwa

• Bowtie

  • singleSM.WGS_NS_N_combine6-9.bowtie.dedup.bam

  • WGS_NS_6-9N_vs_1-5T.bowtie.syntheticTumor.bam

  • WGS_NS_6-9N_vs_1-5T.bowtie.synthetic_snvs.vcf

  • WGS_NS_6-9N_vs_1-5T.bowtie.synthetic_indels.leftAlign.vcf

  • TNscope: TNscope 201711.02 - WGS_NS_6-9N_vs_1-5T.bowtie

• NovoAlign

  • singleSM.WGS_NS_N_combine6-9.novo.dedup.bam

  • WGS_NS_6-9N_vs_1-5T.novo.syntheticTumor.bam

  • WGS_NS_6-9N_vs_1-5T.novo.synthetic_snvs.vcf

  • WGS_NS_6-9N_vs_1-5T.novo.synthetic_indels.leftAlign.vcf

  • TNscope: TNscope 201711.02 - WGS_NS_6-9N_vs_1-5T.novo

Genentech 300X SPP

• BWA

  • Tumor: Genentech.300X.Tumor.bwa.dedup.bam

  • Normal: Genentech.300X.Normal.bwa.dedup.bam

  • In silico tumor: Genentech.SPP.300X.bwa.bamSplit01.syntheticTumor.bam

  • In silico normal: Genentech.SPP.300X.bwa.bamSplit01.syntheticNormal.bam

  • ground truth snv: Genentech.SPP.300X.bwa.bamSplit01.synthetic_snvs.vcf

  • ground truth indel: Genentech.SPP.300X.bwa.bamSplit01.synthetic_indels.leftAlign.vcf

• Bowtie

  • Tumor: Genentech.300X.Tumor.bowtie.dedup.bam

  • Normal: Genentech.300X.Normal.bowtie.dedup.bam

  • In silico tumor: Genentech.SPP.300X.bowtie.bamSplit01.syntheticTumor.bam

  • In silico normal: Genentech.SPP.300X.bowtie.bamSplit01.syntheticNormal.bam

  • ground truth snv: Genentech.SPP.300X.bowtie.bamSplit01.synthetic_snvs.vcf

  • ground truth indel: Genentech.SPP.300X.bowtie.bamSplit01.synthetic_indels.leftAlign.vcf

• NovoAlign

  • Tumor: Genentech.300X.Tumor.novo.dedup.bam

  • Normal: Genentech.300X.Normal.novo.dedup.bam

  • In silico tumor: Genentech.SPP.300X.novo.bamSplit01.syntheticTumor.bam

  • In silico normal: Genentech.SPP.300X.novo.bamSplit01.syntheticNormal.bam

  • ground truth snv: Genentech.SPP.300X.novo.bamSplit01.synthetic_snvs.vcf

  • ground truth indel: Genentech.SPP.300X.novo.bamSplit01.synthetic_indels.leftAlign.vcf