Should at least one mutation id overlap between any two of the input samples?
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lincj1994 commented
Hi. I have run pyclone on over 800 samples and it reported an error: No mutations found in common across samples. But some of the samples had overlapped mutation_id.
> CBCGA_pyclone2[duplicated(CBCGA_pyclone2$mutation_id), ][1:10, ]
Tumor_Sample_Barcode mutation_id ref_counts var_counts normal_cn minor_cn major_cn
1070 FHCJ 3:179234297:179234297:A:G 65 129 2 0 3
1620 GACY 3:179234297:179234297:A:G 55 49 2 0 3
1984 IUJD 3:179234297:179234297:A:G 69 11 2 1 2
2324 QMXZ 3:179234297:179234297:A:G 260 283 2 2 3
2520 KQSA 3:179234297:179234297:A:G 133 50 2 1 1
2693 JYNK 3:49375540:49375540:C:T 156 76 2 1 1
3104 MHWZ 3:179218294:179218294:G:A 42 12 2 2 2
3172 XTZG 3:179234297:179234297:A:G 112 19 2 1 2
3229 YAWJ 3:179234297:179234297:A:G 98 11 2 1 1
3344 YPQD 11:56470012:56470012:G:A 112 10 2 1 1