Comments (11)
from accucopy.
This inference output (infer.out.tsv) shows
purity ploidy ploidy_naive rc_ratio_of_cp_2 segment_stddev_divider snp_maf_stddev_divider snp_coverage_min snp_coverage_var_vs_mean_ratio period_discover_run_type no_of_peaks_for_logL
0.10768 1.9197 1.9444 1003 20 20 2 10 1 3
logL period best_no_of_copy_nos_bf_1st_peak first_peak_int
1.7805e+07 54 1 948
no_of_segments no_of_segments_used no_of_snps no_of_snps_used
171 171 1660150 1660045
The tre histogram and cnv plot show that
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Thank you for your help.
This is "infer.status.txt" file
### candidate period_int: 54
Finding first peak, period_int: 54, within bounds of (10-1063)...
best_first_peak center: 951
sum of window count at all periodic peaks: 1.68742e+06
half_width_int: 9
Find_first_peak_ab_init() for period: 54
first peak: 951
lower bound: 942
upper bound: 960
Tallest peak index=1, peak_center_int=1003, no_of_windows=4635697.
First peak's peak_index=0, peak_center_int=948, no_of_windows=1580.
no_of_copy_nos_bf_1st_peak_prior=1
max_no_of_copy_nos_bf_1st_peak=1
best_logL_snp: -1.60619e+06
no_of_peaks_for_logL: 3
purity: 0.107677
ploidy: 1.94444
logL: 1.78047e+07
### candidate period_int: 179
Finding first peak, period_int: 179, within bounds of (10-1094)...
best_first_peak center: 1005
sum of window count at all periodic peaks: 1.68649e+06
half_width_int: 12
Find_first_peak_ab_init() for period: 179
first peak: 1005
lower bound: 993
upper bound: 1017
Tallest peak index=0, peak_center_int=1003, no_of_windows=4635697.
First peak's peak_index=0, peak_center_int=1003, no_of_windows=4635697.
no_of_copy_nos_bf_1st_peak_prior=2
max_no_of_copy_nos_bf_1st_peak=2
best_logL_snp: -1.60556e+06
no_of_peaks_for_logL: 3
purity: 0.356929
ploidy: 1.98324
logL: 1.77938e+07
### Best period from likelihood: 54
best_purity: 0.107677
best_ploidy: 1.94444
Q: 1003
logL: 1.78047e+07
best_no_of_copy_nos_bf_1st_peak: 1
first_peak_center: 948
first_peak_half_width: 11
Outputting copy number to /mnt/INPUT/OS0130_PC_Accucopy_output/cnv.output.tsv
copy number: 1
copy number: 2
copy number: 3
copy number: 4
copy number: 5
copy number: 6
copy number: 7
copy number: 8
copy number: 9
copy number: 10
copy number: 11
copy number: 12
copy number: 13
copy number: 14
copy number: 15
copy number: 16
copy number: 17
copy number: 18
copy number: 19
copy number: 20
copy number: 21
copy number: 22
copy number: 23
copy number: 24
copy number: 25
copy number: 26
copy number: 27
copy number: 28
copy number: 29
copy number: 30
copy number: 31
copy number: 32
copy number: 33
copy number: 34
copy number: 35
copy number: 36
copy number: 37
copy number: 38
For subclone regions
Warning: For segment chr1: 124616001-124912000. The no_of_snps, -1, <=0. So skip calculate for that segment.
Warning: For segment chr1: 121887501-122738000. The no_of_snps, -1, <=0. So skip calculate for that segment.
CNV output done. ploidy_cnv_all=1.91968 ploidy_clonal=1.99458
Outputting logL ...Done.
Outputting SNP logORs by peaks to /mnt/INPUT/OS0130_PC_Accucopy_output/snp_logOR_by_peak.tsv ... 9 peaks with valid data.
Outputting RC ratio of peaks to /mnt/INPUT/OS0130_PC_Accucopy_output/rc_ratios_of_peaks_of_best_period.tsv ... 762 segments.
Outputting peak bounds to /mnt/INPUT/OS0130_PC_Accucopy_output/peak_bounds.tsv ... 38 peaks.
from accucopy.
For more information about my samples, the tumor sample is WGS with 60X coverage, and matched normal is WGS with 30X coverage. Matched normal also contains driver mutations (TP53).
We estimate that tumor purity should be > 90% by cell morphology observation.
However, this purity estimate is conflict with the purity estimated by Accucopy.
Is there any parameter that I should modify to make the Accucopy model fit more to my sample?
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from accucopy.
ok, looking forward to see your update. Thank you for your nice work.
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Very useful,
I will try this new option soon. Thank you very much.
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Related Issues (20)
- Licensing issues HOT 8
- Run on long reads data? HOT 2
- Lacking python3 packages in docker HOT 5
- Suggestion on input bams? HOT 2
- Empty Output HOT 3
- maestre: libbz2.so.1.0 not found HOT 2
- Bug at "--period" option HOT 4
- [ERROR] [normalize] Error Message HOT 5
- caller_path HOT 1
- unable to infer tumour purity HOT 4
- input to pyclone-vi HOT 1
- unable to open file: name = '/data/modif_genome_test1/model_selection_l og/model_selection.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0 HOT 7
- CNV.output.tsv not generated HOT 3
- https://www.yfish.org/display/PUB/Accucopy is missing (404) HOT 2
- can accucopy support create a baseline by normal samples and then use tumor only samples? HOT 1
- unmatched chromosome name get error HOT 6
- Failed to complete command task: 'rm_individual_seg_files' launched from master workflow, HOT 11
- Stuck at reduce_all_segments HOT 1
- Exception in thread TaskFileWriter-Thread: HOT 7
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from accucopy.