Data Analysis
Somatic mutation reference call sets for the HCC1395 vs. HCC1395BL reference samples
A key objective of the working group is to establish reference call sets for somatic mutation detections (SNV and Indel). The detailed procedures were documented as High-confidence Somatic SNV and INDEL v1.2.
Code to create the reference call set are deposited in the seqc2 branch of SomaticSeq.
Latest release for the reference call set can be found here, or copy the ftp link directly below
All the raw sequencing data can be found at Sequencing.
BWA MEM aligned BAM files can also be found here.
2021 MAQC Society 4th Annual Meeting
Establishing community reference samples, data, and call sets for benchmarking cancer mutation detection using whole-genome sequencing
-- presented by Li Tai Fang
Links to resources used for analysis
SNV and small indel calling
These mutation callers were used:
MuTect2 4.beta.6
SomaticSniper v1.0.5.0
VarDictJava v1.5.1
MuSE v1.0rc_c
Strelka v2.8.2
TNscope 201711.02
SomaticSeq and NeuSomatic were run after those individual callers generated somatic mutation candidates.
Li Tai Fang has created automated run scripts to run their dockerized tools. They're documented here.
Data storage and computation resources
We used Globus for internal data sharing. Here is some documentation of setting it up.