-
Notifications
You must be signed in to change notification settings - Fork 18
Walk through tutorial
Brian Haas edited this page Mar 2, 2021
·
16 revisions
Please be sure to have installed the CTAT-Mutations Pipeline software including setting up the CTAT genome library before running the pipeline.
Use the following command to run the pipeline, using the sample data provided in the testing/ subdirectory that's included with the ctat_mutations software.
python /path/to/ctat_mutations \
--left reads_1.fastq.gz \
--right reads_2.fastq.gz \
--out_dir varcalling.outdir
Note, this step might take ~30 minutes to complete.
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 clinvar_sig TUMOR TISSUE COSMIC_ID FATHMM chasmplus_pval vest_pval mupit_link
chr1 11130632 G T MTOR 59 745.6399999999999 60 NA carcinoma_--_adenocarcinoma lung COSV63879124 PATHOGENIC 0.0606 0.44247 "http://www.cravat.us/MuPIT_Interactive?gm=chr1:11130632"
chr1 11130740 A C MTOR 62 202.64 60 NA carcinoma_--_adenocarcinoma lung COSV63872139 PATHOGENIC 4.76e-05 0.04777 "http://www.cravat.us/MuPIT_Interactive?gm=chr1:11130740"
chr1 26774594 C T ARID1A 23 303.64 60 NA malignant_melanoma_--_acral_lentiginous skin COSV61383982 PATHOGENIC 1.6e-06 0.01528 NA
chr1 114716123 C T NRAS 259 6233.06 60 "Pathogenic" haematopoietic_neoplasm_--_acute_myeloid_leukaemia haematopoietic_and_lymphoid_tissue COSV54736416 PATHOGENIC 0 NA "http://www.cravat.us/MuPIT_Interactive?gm=chr1:114716123"
chr2 177234087 T A NFE2L2 81 1812.06 60 NA carcinoma_--_NS liver COSV67960411 PATHOGENIC 0 0.00344 "http://www.cravat.us/MuPIT_Interactive?gm=chr2:177234087"
chr2 201286575 T G CASP8 19 360.98 60 NA carcinoma_--_adenocarcinoma large_intestine COSV51852791 PATHOGENIC 3.2e-06 0.00536 "http://www.cravat.us/MuPIT_Interactive?gm=chr2:201286575"
chr2 208248388 C T IDH1 51 357.64 60 "Pathogenic" glioma_--_oligodendroglioma_Grade_III central_nervous_system COSV61615239 PATHOGENIC 0 0.02014 "http://www.cravat.us/MuPIT_Interactive?gm=chr2:208248388"
chr3 49375540 C T RHOA 646 5072.64 60 NA carcinoma_--_adenocarcinoma large_intestine COSV69041693 PATHOGENIC 3.15e-05 0.01042 "http://www.cravat.us/MuPIT_Interactive?gm=chr3:49375540"
chr3 179218303 G A PIK3CA 19 145.64 60 "Pathogenic/Likely-pathogenic" carcinoma_--_papillary_carcinoma thyroid COSV55873239 PATHOGENIC 0 NA "http://www.cravat.us/MuPIT_Interactive?gm=chr3:179218303"
chr5 68293360 C T PIK3R1 26 216.64 60 "Benign/Likely-benign" carcinoma_--_NS breast COSV57123112 PATHOGENIC NA NA NA
chr5 112780896 G A APC 7 70.64 60 "Uncertain-significance" carcinoma_--_adenocarcinoma stomach COSV57397660 PATHOGENIC 0.000105 0.05192 "http://www.cravat.us/MuPIT_Interactive?gm=chr5:112780896"
chr7 55191831 T A EGFR 190 675.6399999999999 60 "Pathogenic/Likely-pathogenic,-drug-response" carcinoma_--_non_small_cell_carcinoma lung COSV51766344 PATHOGENIC 0 0.0082 "http://www.cravat.us/MuPIT_Interactive?gm=chr7:55191831"
chr12 25245350 C A KRAS 24 261.64 60 "Pathogenic" carcinoma_--_adenocarcinoma large_intestine COSV55497419 PATHOGENIC 0 0.01002 "http://www.cravat.us/MuPIT_Interactive?gm=chr12:25245350"
chr12 112450394 G T PTPN11 65 275.64 60 "Pathogenic" glioma_--_astrocytoma_Grade_III central_nervous_system COSV61004869 PATHOGENIC 6.4e-07 0.01609 "http://www.cravat.us/MuPIT_Interactive?gm=chr12:112450394"
chr14 95103424 C T DICER1 10 252.06 60 "Benign/Likely-benign" carcinoma_--_endometrioid_carcinoma endometrium COSV58615839 PATHOGENIC NA NA NA
chr16 3781283 C T CREBBP 23 79.64 60 NA carcinoma_--_adenocarcinoma large_intestine COSV52114432 PATHOGENIC 0.00543 0.92066 NA
chr16 68813455 C A CDH1 96 617.64 60 NA carcinoma_--_squamous_cell_carcinoma oesophagus COSV55737831 PATHOGENIC 5.44e-05 0.00557 NA
chr17 7674221 G A TP53 26 737.06 60 "Pathogenic" carcinoma_--_NS urinary_tract COSV52662035 PATHOGENIC 0 0.00071 "http://www.cravat.us/MuPIT_Interactive?gm=chr17:7674221"
chr17 39723967 T C ERBB2 80 967.64 60 "Likely-pathogenic" carcinoma_--_lobular_carcinoma breast COSV54062780 PATHOGENIC 0 0.00293 "http://www.cravat.us/MuPIT_Interactive?gm=chr17:39723967"
chr19 12690014 T G FBXW9 42 156.64 60 NA Ewings_sarcoma-peripheral_primitive_neuroectodermal_tumour_--_NS bone COSV66709239 PATHOGENIC 0.306 0.15899 "http://www.cravat.us/MuPIT_Interactive?gm=chr19:12690014"
chr19 52216574 T C PPP2R1A 3 54.84 60 NA NA NA NA NA 0.0178 0.03623 "http://www.cravat.us/MuPIT_Interactive?gm=chr19:52216574"
chr22 41170455 T A EP300 19 134.64 60 NA glioma_--_astrocytoma_Grade_IV central_nervous_system COSV54331178 PATHOGENIC 0 NA "http://www.cravat.us/MuPIT_Interactive?gm=chr22:41170455"
The corresponding interactive igv-js.html report is available as variants.HC_hard_cutoffs_applied.cancer.igvjs_viewer.html. Just right-click, save-as, and open up the html file in your web browser.