Last active
August 29, 2015 14:16
-
-
Save gatoravi/e760ea98c560a059dde9 to your computer and use it in GitHub Desktop.
define models for imported instrument data.
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| #List all the instrument-data that is imported | |
| genome instrument-data list imported "sample.patient.common_name='TST1ds' and sample.extraction_type = 'genomic dna'" | |
| genome instrument-data list imported "sample.patient.common_name='TST1ds' and sample.extraction_type = 'rna'" | |
| #Define the models based on imported instrument-data, rename the ID's | |
| genome model define rna-seq --reference-sequence-build='106942997' --annotation-build='124434505' --cancer-annotation-db='tgi/cancer-annotation/human/build37-20131010.1' --subject='H_NJ-HCC1395ds-HCC1395_RNA' --processing-profile='2762841' --instrument-data='0296e0aeeb3f4daab1e8604cddb2cb70' --model-name='hcc1395ds-tumor-rnaseq' | |
| genome model define rna-seq --reference-sequence-build='106942997' --annotation-build='124434505' --cancer-annotation-db='tgi/cancer-annotation/human/build37-20131010.1' --subject='H_NJ-HCC1395ds-HCC1395_BL_RNA' --processing-profile='2762841' --instrument-data='675561c466744c8498f903b77ee9acbe' --model-name='hcc1395ds-normal-rnaseq' | |
| genome model define reference-alignment --reference-sequence-build='106942997' --annotation-reference-build='124434505' --subject='H_NJ-HCC1395ds-HCC1395' --processing-profile='2635769' --dbsnp-build='127786607' --target-region-set-names='NimbleGen v3 Capture Chip Set' --region-of-interest-set-name='NimbleGen v3 Capture Chip Set' --instrument-data='4d012edfdb154310a2e390ce3c47b26c' --model-name='hcc1395ds-tumor-refalign-exome' | |
| genome model define reference-alignment --reference-sequence-build='106942997' --annotation-reference-build='124434505' --subject='H_NJ-HCC1395ds-HCC1395' --processing-profile='2635769' --dbsnp-build='127786607' --instrument-data='7bb1ff78eea545dba8b5909276d83bc1,ee9fd6cec05046248ee45b30e79ff7e8,f0e9afd3b8f84952923ceb4f761e762a,85a6d2d6d1b64d2d881c7f2558629432,a750da970d7d4f19ae5ab0e8eb18a94d' --model-name='hcc1395ds-tumor-refalign-wgs' | |
| genome model define reference-alignment --reference-sequence-build='106942997' --annotation-reference-build='124434505' --subject='H_NJ-HCC1395ds-HCC1395_BL' --processing-profile='2635769' --dbsnp-build='127786607' --target-region-set-names='NimbleGen v3 Capture Chip Set' --region-of-interest-set-name='NimbleGen v3 Capture Chip Set' --instrument-data='3562f8ead8bf4a8881f773184f6f22d1' --model-name='hcc1395ds-normal-refalign-exome' | |
| genome model define reference-alignment --reference-sequence-build='106942997' --annotation-reference-build='124434505' --subject='H_NJ-HCC1395ds-HCC1395_BL' --processing-profile='2635769' --dbsnp-build='127786607' --instrument-data='667e244fbb90442badfa78eebe717302,5ca9c666406544bc971108d110fa02f2,b41e2ea9d3d14fd2a063956c896b9544' --model-name='hcc1395ds-normal-refalign-wgs' | |
| genome model define somatic-variation --tumor-model='hcc1395-tumor-refalign-exome' --normal-model='hcc1395-normal-refalign-exome' --processing-profile=2762563 --annotation-build=124434505 --previously-discovered-variations-build=127786607 --model-name='hcc1395ds-somatic-exome' | |
| genome model define somatic-variation --tumor-model='hcc1395-tumor-refalign-wgs' --normal-model='hcc1395-normal-refalign-wgs' --processing-profile=2762563 --annotation-build=124434505 --previously-discovered-variations-build=127786607 --model-name='hcc1395ds-somatic-wgs' |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment