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Roth-Lab / pyclone

Probabilistic model for inferring clonal population structure from deep NGS sequencing.
https://bitbucket.org/aroth85/pyclone/wiki/Home
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Should at least one mutation id overlap between any two of the input samples? #24

Open lincj1994 opened 2 years ago

lincj1994 commented 2 years ago

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