Running the ACCESS snps_and_indels.cwl workflow

quickstart.md

Commands to run ACCESS snps and indels pipeline

Note: the version here pipeline_VariantCalling will be subject to change

1. Activate the virtual environment

Note that if you are working off of your own clone of the project, you must create your own virtual environment and install the pipeline there (see steps 1-4 in the readme).

source /home/johnsoni/virtualenvs/pipeline_VariantCalling/bin/activate
source /home/johnsoni/pipeline_VariantCalling/ACCESS-Pipeline/python_tools/pipeline_kickoff/workspace_init.sh

2. Generate the inputs file (three options)

Note that the Bams must have Sample IDs in their filenames, and if using matched mode, these Sample IDs must match the IDs in the -p pairing file.

Description of parameters:

---

• -o Name of inputs file to be generated

• -pn Project Name

• -dn Default Normal - Will be used in unmatched_mode (-m), or if normal_id from pairing file is blank while in matched mode. Typically, this is a duplex, high-depth plasma, and is chosen from the list of curated bams (-cbd).

• -tb Duplex Tumor Bams directory - Only tumor bams to be used in variant calling should be present here. No normals should be present here.

• -sb Simplex Tumor Bams directory - Each duplex tumor bam from the -tb directory must have an associated simplex bam in this directory.

• -cbd Curated Duplex Bams - Duplex bams to be genotyped for all mutations found in the -tb tumor bams directory.

• -cbs Curated Simplex Bams - Simplex bams which are associated 1:1 with -cbd curated bams.

• -m Matched mode

• -p Pairing file - If in matched mode, this will be used for variant calling and genotyping. If in unmatched mode, this will only be used for genotyping.

• -nb Normal Bams directory (if in matched mode). Typically these are either unfiltered bams, or Impact Normal bams.

---

Option 1: Unmatched variant calling, unmatched genotyping:

generate_access_variants_inputs \
-o inputs.yaml \
-pn my_project_name \
-dn /ifs/work/bergerm1/brannona/ACCESS/ACCESSv1-VAL-20180034/duplex_bams/F22_S2_001_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-duplex.bam \
-tb /ifs/work/bergerm1/Innovation/sandbox/Maysun/VariantCallingTeam/ValidationRedo/Bams/duplex-bams \
-sb /ifs/work/bergerm1/Innovation/sandbox/Maysun/VariantCallingTeam/ValidationRedo/Bams/simplex-bams \
-cbd /ifs/work/bergerm1/Innovation/projects/Maysun/custom-capture/GIST/Analysis/5500-FR/all_samples/curated_duplex/ \
-cbs /ifs/work/bergerm1/Innovation/projects/Maysun/custom-capture/GIST/Analysis/5500-FR/all_samples/curated_simplex/

Option 2: Unmatched variant calling, matched genotyping:

Include a pairing file -p (see example at /home/johnsoni/test_pairs.tsv), and -nb for paired normal bams folder:

generate_access_variants_inputs \
-o inputs.yaml \
-pn my_project_name \
-dn /ifs/work/bergerm1/brannona/ACCESS/ACCESSv1-VAL-20180002/duplex_bams/M16-26666_S9_001_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-duplex.bam \
-tb /ifs/work/bergerm1/Innovation/sandbox/Maysun/VariantCallingTeam/ValidationRedo/Bams/duplex-bams \
-nb /ifs/work/bergerm1/Innovation/sandbox/Maysun/VariantCallingTeam/ValidationRedo/Bams/duplex-normal-bams \
-sb /ifs/work/bergerm1/Innovation/sandbox/Maysun/VariantCallingTeam/ValidationRedo/Bams/simplex-bams \
-cbd /ifs/work/bergerm1/Innovation/projects/Maysun/custom-capture/GIST/Analysis/5500-FR/all_samples/curated_duplex/ \
-cbs /ifs/work/bergerm1/Innovation/projects/Maysun/custom-capture/GIST/Analysis/5500-FR/all_samples/curated_simplex/ \
-p /path/to/pairing_file.tsv

Option 3: Matched variant calling, matched genotyping:

Include a pairing file -p (see example at /home/johnsoni/test_pairs.tsv), -m for matched mode, and -nb for paired normal bams folder:

generate_access_variants_inputs \
-o inputs.yaml \
-pn my_project_name \
-dn /ifs/work/bergerm1/brannona/ACCESS/ACCESSv1-VAL-20180002/duplex_bams/M16-26666_S9_001_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-duplex.bam \
-tb /ifs/work/bergerm1/Innovation/sandbox/Maysun/VariantCallingTeam/ValidationRedo/Bams/duplex-bams \
-nb /ifs/work/bergerm1/Innovation/sandbox/Maysun/VariantCallingTeam/ValidationRedo/Bams/duplex-normal-bams \
-sb /ifs/work/bergerm1/Innovation/sandbox/Maysun/VariantCallingTeam/ValidationRedo/Bams/simplex-bams \
-cbd /ifs/work/bergerm1/Innovation/projects/Maysun/custom-capture/GIST/Analysis/5500-FR/all_samples/curated_duplex/ \
-cbs /ifs/work/bergerm1/Innovation/projects/Maysun/custom-capture/GIST/Analysis/5500-FR/all_samples/curated_simplex/ \
-p /path/to/pairing_file.tsv \
-m

3. Submit the run:

pipeline_submit \
--output_location `pwd` \
--inputs_file inputs.yaml \
--workflow /home/johnsoni/pipeline_VariantCalling/ACCESS-Pipeline/workflows/subworkflows/snps_and_indels.cwl \
--batch_system lsf \
--log_level DEBUG