Walk through tutorial

Please be sure to have installed the CTAT-Mutations Pipeline software including [setting up the CTAT genome library](CTAT-mutations-installation#CTAT-mutations Genome Lib Installation) before running the pipeline.

1. Download and uncompress demo data at

   wget https://data.broadinstitute.org/Trinity/CTAT/mutation/ctat_mutation_demo.tar.gz

   Uncompress and extract data from the tar.gz file

   tar xvf ctat_mutation_demo.tar.gz

2. Use the following command to run the pipeline:

   python ctat-mutations/ctat_mutations \
          --left ctat_mutation_demo_1.fastq \
          --right ctat_mutation_demo_2.fastq \
          --out_dir varcalling.outdir \
          --threads 8 
   

The main output of the pipeline is cancer.tab file. The demo data is a small set of reads and variants used for testing purposes which correspond to breast cancer cell line BT474. Let's take a look at cancer.tab output which lists all the cancer variants with respect to these small set of reads only:

CHROM | POS | REF | ALT | GENE | DP | QUAL | MQ | SAO | NSF | NSM | NSN | TUMOR | TISSUE | COSMIC_ID | KGPROD | RS | PMC | CHASM_PVALUE | CHASM_FDR | VEST_PVALUE | VEST_FDR
----- | ---- | ---- | ---- | ----- | --- | ----- | --- | ---- | ---- | ---- | ---- | ------ | ------- | ---------- | ------- | --- | ---- | ------------- | ---------- | ------------ | ---------
chr5 | 474989 | A | G | LOC100288152,SLC9A3 | 4 | 96.03 | 60 | NA | NA | NA | NA | carcinoma_--_NS | urinary_tract | COSM4006021 | NA | NA | NA | 0.1114 | 0.3 | 0.96802 | 1 
chr5 | 181224474 | G | A | TRIM41 | 45 | 375.77 | 60 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | 0.0694 | 0.3 | 0.48052 | 1 
chr8 | 143923759 | G | A | PLEC | 66 | 878.77 | 60 | NA | NA | NA | NA | carcinoma_--_adenocarcinoma | large_intestine | COSM3750086 | NA | NA | NA | 0.0344 | 0.2 | 0.84202 | 1 
chr12 | 56420869 | G | A | TIMELESS | 48 | 392.77 | 60 | NA | NA | NA | NA | carcinoma_--_adenocarcinoma | large_intestine | COSM3753397 | NA | NA | NA | 0.0744 | 0.3 | 0.18439 | 1 
chr17 | 7673767 | C | T | TP53 | 61 | 2000.77 | 60 | NA | NA | NA | NA | Ewings_sarcoma-peripheral_primitive_neuroectodermal_tumour_--_NS | bone | COSM3717625 | NA | NA | NA | 0 | 0.05 | 0.01447 | 0.3 
chr17 | 7676154 | G | C | TP53 | 80 | 2150.77 | 60 | NA | NA | NA | NA | haematopoietic_neoplasm_--_acute_myeloid_leukaemia | haematopoietic_and_lymphoid_tissue | COSM3766193 | NA | NA | NA | 0.087 | 0.3 | 0.52717 | 1
chr17 | 43071077 | T | C | BRCA1 | 4 | 97.03 | 60 | NA | NA | NA | NA | haematopoietic_neoplasm_--_acute_myeloid_leukaemia | haematopoietic_and_lymphoid_tissue | COSM3755560 | NA | NA | NA | 0.0372 | 0.2 | 0.3446 | 1
chr17 | 43091983 | T | C | BRCA1 | 4 | 89.03 | 60 | NA | NA | NA | NA | haemangioblastoma_--_NS | soft_tissue | COSM3755561 | NA | NA | NA | 0.0002 | 0.05 | 0.64447 | 1
chr17 | 43092919 | G | A | BRCA1 | 2 | 39.74 | 60 | NA | NA | NA | NA | carcinoma_--_NS | prostate | COSM3755564 | NA | NA | NA | 0.0004 | 0.05 | 0.33539 | 1
chr17 | 43093454 | C | T | BRCA1 | 11 | 425.77 | 60 | NA | NA | NA | NA | rhabdomyosarcoma_--_embryonal | soft_tissue | COSM4989394 | NA | NA | NA | 0.0014 | 0.05 | 0.51068 | 1
chr19 | 39177761 | G | C | PAK4 | 107 | 1232.77 | 60 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | 0.0004 | 0.05 | 0.01093 | 0.3
chr19 | 47271515 | T | C | CCDC9 | 12 | 321.77 | 60 | NA | NA | NA | NA | haematopoietic_neoplasm_--_acute_myeloid_leukaemia | haematopoietic_and_lymphoid_tissue | COSM3721172 | NA | NA | NA | 0.093 | 0.3 | 0.97622 | 1
chr20 | 46687147 | C | T | TP53RK | 26 | 453.77 | 60 | NA | NA | NA | NA | carcinoma_--_ductal_carcinoma | pancreas | COSM3758608 | NA | NA | NA | 0.0834 | 0.3 | 0.88584 | 1

All genes such as TRIM41 and BRCA1 listed here are usual mutations sites implicated in Breast cancer.