VisCap
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pughlab
Error running VisCap
I am trying to run VisCap for one of my sample and getting following error, which i can not understand
"/data/Duplication/VisCap-master/MD36//MD36.sample_interval_summary" Error in mat.cov[grep("X", rownames(mat.cov), invert = TRUE), ] : incorrect number of dimensions Calls: make_matrix_from_cov_files -> colSums -> is.data.frame Execution
halted
From the error i could understand there might be a problem with my sample_interval_summary file but i followed the steps shown, and my bed file also seems correct so please help me solve this error
bed file
chr1 46654345 46654440 GENE_ID=POMGNT1_AMPL7155142781 0 +
chr1 46654426 46654514 GENE_ID=POMGNT1_AMPL7154573365 0 +
chr1 46654472 46654555 GENE_ID=POMGNT1_AMPL7154539719 0 +
chr1 46654536 46654657 GENE_ID=POMGNT1_AMPL7153085900 0 +
chr1 46654876 46655005 GENE_ID=POMGNT1_AMPL7153021413 0 +
chr1 46654952 46655042 GENE_ID=POMGNT1_AMPL7155142780 0 +
chr1 46655037 46655159 GENE_ID=POMGNT1_AMPL7153018090 0 +
chr1 46655135 46655257 GENE_ID=POMGNT1_AMPL7153085862 0 +
chr1 46655443 46655571 GENE_ID=POMGNT1_AMPL7154537337 0 +
...
sample_interval_summary file
Target total_coverage average_coverage MDDNA-201_total_cvg MDDNA-201_mean_cvg MDDNA-201_granular_Q1 MDDNA-201_granular_median MDDNA-201_granular_Q3 MDDNA-201_%_above_15
chr1:46654346-46654657 802 2.57 802 2.57 3 4 5 0.0
chr1:46654877-46655257 2309 6.06 2309 6.06 4 7 10 0.0
chr1:46655444-46655667 1410 6.29 1410 6.29 5 8 9 0.0
chr1:46656036-46656267 2314 9.97 2314 9.97 9 12 12 6.9
chr1:46656358-46656479 365 2.99 365 2.99 4 4 4 0.0
chr1:46657702-46657902 444 2.21 444 2.21 1 5 5 0.0
chr1:46657927-46658123 1251 6.35 1251 6.35 2 12 12 0.0
chr1:46658157-46658283 1688 13.29 1688 13.29 13 14 15 22.8
chr1:46658538-46658666 514 3.98 514 3.98 5 5 5 0.0
chr1:46658797-46659080 2914 10.26 2914 10.26 6 9 16 28.5
This may be due to overlapping regions in the bed file. We'll alter the script so it can deal with this in the near future but in the meantime please try with a bed file with no overlapping regions and see if the problem persists.
