Error running VisCap #13
Description
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
Executionhalted
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