Hello,
I am trying to use ExomeCNV to do copy number analysis on exome sequencing data. I have bam files sorted already. I tried to use shell scripts for generating coverage files, one error message came out:
making pileup
[main] The `pileup' command has been removed. Please use `mpileup' instead.
I checked on all of the scripts provided by author, I saw 'pileup' command there, I don't know what that's supposed to mean. Also the coverage files generated from this run are "0" in the last four columns.
command Line I used:
sh bam2coverage.sh sorted.bam exome.bed hg19.fasta script-directory
Thanks,
I am trying to use ExomeCNV to do copy number analysis on exome sequencing data. I have bam files sorted already. I tried to use shell scripts for generating coverage files, one error message came out:
making pileup
[main] The `pileup' command has been removed. Please use `mpileup' instead.
I checked on all of the scripts provided by author, I saw 'pileup' command there, I don't know what that's supposed to mean. Also the coverage files generated from this run are "0" in the last four columns.
command Line I used:
sh bam2coverage.sh sorted.bam exome.bed hg19.fasta script-directory
Thanks,
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