GDC SomaticSniper

The purpose of SomaticSniper is to identify single nucleotide positions that are different between tumor and normal. It takes a tumor bam and a normal bam and compares the two to determine the differences.

Original SomaticSniper: http://gmt.genome.wustl.edu/packages/somatic-sniper/index.html

Docker

There are three Dockerfiles for different purposes:

• Vanilla BAM-readcount
  • /docker/bam-readcount/Dockerfile : BAM-readcount docker without additional features. The bam-readcount will be used for the fpfilter.
• Vanilla SomaticSniper
  • /docker/somaticsniper/Dockerfile : SomaticSniper docker without additional features.
• Multi-threading SomaticSniper
  • /docker/multi_muse/Dockerfile : A python multi-threading implementation on SomaticSniper with builtin LOH and High confidence filtering. To achieve scatter/gather method on Docker level, input needs an array of tumor-normal mpileup from samtools mpileup -f.

How to build

https://docs.docker.com/engine/reference/builder/

The docker images are tested under multiple environments. The most tested ones are:

• Docker version 19.03.2, build 6a30dfc
• Docker version 18.09.1, build 4c52b90
• Docker version 18.03.0-ce, build 0520e24
• Docker version 17.12.1-ce, build 7390fc6

For external users

The repository has only been tested on GDC data and in the particular environment GDC is running in. Some of the reference data required for the workflow production are hosted in GDC reference files. For any questions related to GDC data, please contact the GDC Help Desk at [email protected].

There is a production-ready CWL example at https://github.com/NCI-GDC/somaticsniper-cwl which uses the docker images that are built from the Dockerfiles in this repo.

To use docker images directly or with other workflow languages, we recommend to build and use either vanilla SomaticSniper or multi-threading SomaticSniper.

To run multi-threading SomaticSniper:

[INFO] [20200110 04:32:14] [multi_somaticsniper] - --------------------------------------------------------------------------------
usage: Internal multithreading SomaticSniper calling. [-h] -f REFERENCE_PATH
                                                      -t TUMOR_BAM -n
                                                      NORMAL_BAM -c
                                                      THREAD_COUNT -m MPILEUP
                                                      [-q MAP_Q] [-Q BASE_Q]
                                                      [-L] [-G] [-p] [-J]
                                                      [-s PPS] [-T THETA]
                                                      [-N NHAP] [-r PD]
                                                      [-F FOUT]

optional arguments:
  -h, --help            show this help message and exit
  -f REFERENCE_PATH, --reference_path REFERENCE_PATH
                        Reference path.
  -t TUMOR_BAM, --tumor_bam TUMOR_BAM
                        Tumor bam file.
  -n NORMAL_BAM, --normal_bam NORMAL_BAM
                        Normal bam file.
  -c THREAD_COUNT, --thread_count THREAD_COUNT
                        Number of thread.
  -m MPILEUP, --mpileup MPILEUP
                        A list of normal-tumor samtools mpileup files on
                        different region. Created by "samtools mpileup -f".
                        The file name must contain region. e.g.
                        chr1-1-248956422.mpileup
  -q MAP_Q, --map_q MAP_Q
                        filtering reads with mapping quality less than this
                        value.
  -Q BASE_Q, --base_q BASE_Q
                        filtering somatic snv output with somatic quality less
                        than this value.
  -L, --loh             do not report LOH variants as determined by genotypes
                        (T/F).
  -G, --gor             do not report Gain of Reference variants as determined
                        by genotypes (T/F).
  -p, --psc             disable priors in the somatic calculation. Increases
                        sensitivity for solid tumors (T/F).
  -J, --ppa             Use prior probabilities accounting for the somatic
                        mutation rate (T/F).
  -s PPS, --pps PPS     prior probability of a somatic mutation (implies -J).
  -T THETA, --theta THETA
                        theta in maq consensus calling model (for -c/-g).
  -N NHAP, --nhap NHAP  number of haplotypes in the sample.
  -r PD, --pd PD        prior of a difference between two haplotypes.
  -F FOUT, --fout FOUT  output format (classic/vcf/bed).

For GDC users

See https://github.com/NCI-GDC/gdc-somatic-variant-calling-workflow.