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arihueb
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Nov 24, 2023
| following: mutation cluster assignments (CLUSTER), mutation PhyloCCF estimates (CCF_PHYLO); observed CCF (CCF_OBS); mutation copy number estimates for each mutation in each tumor sample (MUT_COPY); mutation identifier <CASE_ID>:<CHR>:<POS>:<REF>:<ALT> (mutation_id) | ||
| - <CASE_ID>.SCoutput.FULL.tsv: A mutation table in same format as above except with additional column CLEAN, a logical flag indicating whether this mutation was removed (CLEAN==FALSE) | ||
| - <CASE_ID>.removed.muts.txt: A mutation table comprising mutations removed during the clustering stage. This file will not be generated if no mutations are removed. | ||
| - <CASE_ID>_pyclone_cluster_assignment_copynumber_clean.pdf: Genome plots of each mutation plotted at its genomic position (x-axis) vs it's estimated mutation copy number (y-axis) for each tumor sample |
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move this down to the plots section
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