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RahmanTeam / DECoN

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Error in ReadInBams.R GenomicRanges::seqnames(target) #22

Open shethharsh08 opened 4 years ago

shethharsh08 commented 4 years ago

Hello,

I tried to use ReadInBams.R command in Linux to generate the first file. However, I got an error as follows:

Error in GenomicRanges::seqnames(target) : object 'target' not found Calls: getBamCounts ... countBamInGRanges.exomeDepth -> paste0 -> In addition: Warning message: In countBamInGRanges.exomeDepth(bam.file = bam, index = index, granges = target, : Apparently the BAM file uses the convention chr1 instead of 1 for chromosome names, but your target sequence does not. Therefore, adding the chr prefix to the target intervals Execution halted

I am unable to find a way to remove "chr" convention from BAM files. Can you help please?

Thanks!