IndexError

[SebastianHollizeck]

Hey,

with my command

~/PhylogicNDT/PhylogicNDT.py Cluster -i sample_id -sif CA99_input.sif -rb

I get

Traceback (most recent call last):
  File "/home/shollizeck/PhylogicNDT/PhylogicNDT.py", line 342, in <module>
    args.func(args)
  File "/home/shollizeck/PhylogicNDT/Cluster/Cluster.py", line 91, in run_tool
    phylogicoutput.write_patient_mut_ccfs(patient_data, cluster_ccfs)
  File "/home/shollizeck/PhylogicNDT/output/PhylogicOutput.py", line 829, in write_patient_mut_ccfs
    mut_mean, mut_high, mut_low = self._get_mean_high_low(np.array(mut.ccf_1d))
  File "/home/shollizeck/PhylogicNDT/output/PhylogicOutput.py", line 878, in _get_mean_high_low
    elif low == 0 or ccf[high + 1] > ccf[low - 1]:
IndexError: index 5051 is out of bounds for axis 0 with size 101

can you help me fix that?

Cheers, Sebastian

[iglc]

Please check if your input is malformated. Can you provide a header here?

[SebastianHollizeck]

These are the files I used

[shollizeck@vmpr-res-cluster1 test_phylogicNDT]$ cat CA99_input.sif
 sample_id  maf_fn  seg_fn  purity  timepoint
 CA9911 CA99-11.tsv     0.71    0
 CA9926 CA99-26.tsv     0.60    0
 CA9931 CA99-31.tsv     0.15    0
 CA9941 CA99-41.tsv     0.21    0
 CA9947 CA99-47.tsv     0.45    0
 CA9955 CA99-55.tsv     0.37    0
 CA9957 CA99-57.tsv     0.60    0
 CA9959 CA99-57.tsv     0.66    0

and

[shollizeck@vmpr-res-cluster1 test_phylogicNDT]$ head CA99-11.tsv
Hugo_Symbol Chromosome  Start_position  Reference_Allele    Tumor_Seq_Allele2   t_ref_count t_alt_count ccf_0.00    ccf_0.01    ccf_0.02    ccf_0.03    ccf_0.04    ccf_0.05    ccf_0.06    ccf_0.07    ccf_0.08    ccf_0.09    ccf_0.10    ccf_0.11    ccf_0.12    ccf_0.13    ccf_0.14    ccf_0.15    ccf_0.16    ccf_0.17    ccf_0.18    ccf_0.19    ccf_0.20    ccf_0.21    ccf_0.22    ccf_0.23    ccf_0.24    ccf_0.25    ccf_0.26    ccf_0.27    ccf_0.28    ccf_0.29    ccf_0.30    ccf_0.31    ccf_0.32    ccf_0.33    ccf_0.34    ccf_0.35    ccf_0.36    ccf_0.37    ccf_0.38    ccf_0.39    ccf_0.40    ccf_0.41    ccf_0.42    ccf_0.43    ccf_0.44    ccf_0.45    ccf_0.46    ccf_0.47    ccf_0.48    ccf_0.49    ccf_0.50    ccf_0.51    ccf_0.52    ccf_0.53    ccf_0.54    ccf_0.55    ccf_0.56    ccf_0.57    ccf_0.58    ccf_0.59    ccf_0.60    ccf_0.61    ccf_0.62    ccf_0.63    ccf_0.64    ccf_0.65    ccf_0.66    ccf_0.67    ccf_0.68    ccf_0.69    ccf_0.70    ccf_0.71    ccf_0.72    ccf_0.73    ccf_0.74    ccf_0.75    ccf_0.76    ccf_0.77    ccf_0.78    ccf_0.79    ccf_0.80    ccf_0.81    ccf_0.82    ccf_0.83    ccf_0.84    ccf_0.85    ccf_0.86    ccf_0.87    ccf_0.88    ccf_0.89    ccf_0.90    ccf_0.91    ccf_0.92    ccf_0.93    ccf_0.94    ccf_0.95    ccf_0.96    ccf_0.97    ccf_0.98    ccf_0.99    ccf_1.00
UNKNOWN 10  107969  T   C   66  1
UNKNOWN 10  168689  C   T   75  0
UNKNOWN 10  387459  A   C   76  1
UNKNOWN 10  414108  G   T   33  0
UNKNOWN 10  430991  T   G   75  0
UNKNOWN 10  493860  T   G   47  0
UNKNOWN 10  541819  C   A   64  0
UNKNOWN 10  548907  G   A   66  0
UNKNOWN 10  551557  T   G   80  0

[iglc]

You don't seem to have any input CCF values?

On Thu, Nov 14, 2019 at 9:38 PM SebastianHollizeck notifications@github.com wrote:

These are the files I used

[shollizeck@vmpr-res-cluster1 test_phylogicNDT]$ cat CA99_input.sif sample_id maf_fn seg_fn purity timepoint CA9911 CA99-11.tsv 0.71 0 CA9926 CA99-26.tsv 0.60 0 CA9931 CA99-31.tsv 0.15 0 CA9941 CA99-41.tsv 0.21 0 CA9947 CA99-47.tsv 0.45 0 CA9955 CA99-55.tsv 0.37 0 CA9957 CA99-57.tsv 0.60 0 CA9959 CA99-57.tsv 0.66 0

and

[shollizeck@vmpr-res-cluster1 test_phylogicNDT]$ head CA99-11.tsv Hugo_Symbol Chromosome Start_position Reference_Allele Tumor_Seq_Allele2 t_ref_count t_alt_count ccf_0.00 ccf_0.01 ccf_0.02 ccf_0.03 ccf_0.04 ccf_0.05 ccf_0.06 ccf_0.07 ccf_0.08 ccf_0.09 ccf_0.10 ccf_0.11 ccf_0.12 ccf_0.13 ccf_0.14 ccf_0.15 ccf_0.16 ccf_0.17 ccf_0.18 ccf_0.19 ccf_0.20 ccf_0.21 ccf_0.22 ccf_0.23 ccf_0.24 ccf_0.25 ccf_0.26 ccf_0.27 ccf_0.28 ccf_0.29 ccf_0.30 ccf_0.31 ccf_0.32 ccf_0.33 ccf_0.34 ccf_0.35 ccf_0.36 ccf_0.37 ccf_0.38 ccf_0.39 ccf_0.40 ccf_0.41 ccf_0.42 ccf_0.43 ccf_0.44 ccf_0.45 ccf_0.46 ccf_0.47 ccf_0.48 ccf_0.49 ccf_0.50 ccf_0.51 ccf_0.52 ccf_0.53 ccf_0.54 ccf_0.55 ccf_0.56 ccf_0.57 ccf_0.58 ccf_0.59 ccf_0.60 ccf_0.61 ccf_0.62 ccf_0.63 ccf_0.64 ccf_0.65 ccf_0.66 ccf_0.67 ccf_0.68 ccf_0.69 ccf_0.70 ccf_0.71 ccf_0.72 ccf_0.73 ccf_0.74 ccf_0.75 ccf_0.76 ccf_0.77 ccf_0.78 ccf_0.79 ccf_0.80 ccf_0.81 ccf_0.82 ccf_0.83 ccf_0.84 ccf_0.85 ccf_0.86 ccf_0.87 ccf_0.88 ccf_0.89 ccf_0.90 ccf_0.91 ccf_0.92 ccf_0.93 ccf_0.94 ccf_0.95 ccf_0.96 ccf_0.97 ccf_0.98 ccf_0.99 ccf_1.00 UNKNOWN 10 107969 T C 66 1 UNKNOWN 10 168689 C T 75 0 UNKNOWN 10 387459 A C 76 1 UNKNOWN 10 414108 G T 33 0 UNKNOWN 10 430991 T G 75 0 UNKNOWN 10 493860 T G 47 0 UNKNOWN 10 541819 C A 64 0 UNKNOWN 10 548907 G A 66 0 UNKNOWN 10 551557 T G 80 0

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[SebastianHollizeck]

As the guide said

the .maf should contain pre-computed raw ccf histograms based on mutations alt/ref count, local copy-number and sample purity (Absolute annotated mafs or .Rdata files are also supported) if the ccf histograms are absent - PhylogicNDT will attempt to compute them from available mutation info as above

I left the ccf values empty

[iglc]

But then you need local absolute copy number data for each mutation. Do you have that?

On Thu, Nov 14, 2019 at 10:22 PM SebastianHollizeck < notifications@github.com> wrote:

As the guide said

the .maf should contain pre-computed raw ccf histograms based on mutations alt/ref count, local copy-number and sample purity (Absolute annotated mafs or .Rdata files are also supported) if the ccf histograms are absent - PhylogicNDT will attempt to compute them from available mutation info as above

I left the ccf values empty

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/broadinstitute/PhylogicNDT/issues/9?email_source=notifications&email_token=ABTLJRG233KRLQZTAC3UTFTQTYIVXA5CNFSM4I6KEN3KYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEEEFJ4Q#issuecomment-554194162, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABTLJRG6DVAE3YHNGRSRT5TQTYIVXANCNFSM4I6KEN3A .

[SebastianHollizeck]

I do have that yes

[mkinnaman]

Sorry - to close out this thread - if you have local absolute copy number data - should those be added to the maf file? 2 columns with nmin and and nmaj?