I have some problems in sample1.covg that is the part of genome music calc-covg.
#Gene Length Covered AT_covd CG_covd CpG_covd
xuhb 13 13 0 0 0
Why the AT_covd CG_covg CpG_covd is zero???what happened with them?
My roi file has one line.
1 3 15 xuhb
My seq.fa is as follows:
My normal.fq is as follows:
My tumor.fq is as follows:
My bam-list file has one line as follows:
sample1 normal.bam tumor.bam
The command which i use is as follows:
genome music bmr calc-covg --bam-list bam1-list --output-dir ex1 --reference-sequence seq.fa --roi-file roi --normal-min-depth 1 --tumor-min-depth 1 --min-mapq 0;
Thank you very much.I am so worry about that problems.