Tumor Heterogeneity Analysis (THetA) and THetA2 are algorithms that estimate the tumor purity and clonal/subclonal copy number aberrations directly from high-throughput DNA sequencing data. This repository includes the updated algorithm, called THetA2.
I'm doing copy number analysis using CNVkit and THeTA2
I ran THetA2 using 43 samples on April 23rd, 40 samples were completed in about a day,
but work on the 3 samples is still running (May 19th)
here's my log
Reading in query file...
Frac with potential copy numbers: 0.876086346237
Reading SNP file at /bio/scratch/starz77/sylee/CNV_TP/P7/P7_T.bwamem.sorted.dedup.realn.recal.dedup.tumor.snp_formatted.txt
Reading SNP file at /bio/scratch/starz77/sylee/CNV_TP/P7/P7_T.bwamem.sorted.dedup.realn.recal.dedup.normal.snp_formatted.txt
Reading interval file at /bio/scratch/starz77/sylee/CNV_TP/P7/P7.theta.interval_count
Calculating BAFs
Determining heterozygosity.
Calculating BAFs.
First round of clustering...
Begin meta clustering...
Classifying clusters...
Plotting classifications...
Determining copy number bounds...
Plotting clusters...
WARNING: Was unable to remove bnpy output. This can be manually removed after THetA has completed. bnpy output has been stored in ./P7_2_cluster_data/
Selecting meta-intervals...
Selected 13 intervals for analysis.
Preprocessing data...
Writing bounds file to ./P7.n2.withBounds
Estimating time...
Estimated Total Time: 88 hour(s)
Performing optimization...
Hello,
I'm doing copy number analysis using CNVkit and THeTA2
I ran THetA2 using 43 samples on April 23rd, 40 samples were completed in about a day,
but work on the 3 samples is still running (May 19th)
here's my log
Reading in query file... Frac with potential copy numbers: 0.876086346237 Reading SNP file at /bio/scratch/starz77/sylee/CNV_TP/P7/P7_T.bwamem.sorted.dedup.realn.recal.dedup.tumor.snp_formatted.txt Reading SNP file at /bio/scratch/starz77/sylee/CNV_TP/P7/P7_T.bwamem.sorted.dedup.realn.recal.dedup.normal.snp_formatted.txt Reading interval file at /bio/scratch/starz77/sylee/CNV_TP/P7/P7.theta.interval_count Calculating BAFs Determining heterozygosity. Calculating BAFs. First round of clustering... Begin meta clustering... Classifying clusters... Plotting classifications... Determining copy number bounds... Plotting clusters... WARNING: Was unable to remove bnpy output. This can be manually removed after THetA has completed. bnpy output has been stored in ./P7_2_cluster_data/ Selecting meta-intervals... Selected 13 intervals for analysis. Preprocessing data... Writing bounds file to ./P7.n2.withBounds Estimating time... Estimated Total Time: 88 hour(s) Performing optimization...
thank you.