About this，I have two questions:
(1) What is the -t option in the callCNV.sh? In our callCNV, do we need a reference? Whether or not -t mean the cancer sample, -c mean the normal sample?
(2) The -c is "GBM3_seq1_2.pfilter.tn5.srt.avg_cov.w1000K_s500K.bed" in your example, which is the smoothBw.sh result. And run the readsMasker.sh to filter out reads or frags in peak regions and get background frags. Why the -c of callCNV.sh is not the filter.bed get from readsMasker.sh?
Finally, is it convenient to provide a complete test script and data set?
Thanks!
About this，I have two questions: (1) What is the -t option in the callCNV.sh? In our callCNV, do we need a reference? Whether or not -t mean the cancer sample, -c mean the normal sample? (2) The -c is "GBM3_seq1_2.pfilter.tn5.srt.avg_cov.w1000K_s500K.bed" in your example, which is the smoothBw.sh result. And run the readsMasker.sh to filter out reads or frags in peak regions and get background frags. Why the -c of callCNV.sh is not the filter.bed get from readsMasker.sh?
Finally, is it convenient to provide a complete test script and data set? Thanks!