Error in using getBamCounts

vplagnol / ExomeDepth

ExomeDepth R package for the detection of copy number variants in exomes and gene panels using high throughput DNA sequencing data.

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Error in using getBamCounts #38

Open Martaprf opened 3 years ago

Martaprf commented 3 years ago

Hi,

I am trying to get the counts in my data but when I run getBamCounts I have the followed error: Error in countBamInGRanges.exomeDepth(bam.file = bam, index = index, granges = target, : Some sequences in the target data frame cannot be found in the index of the BAM file

Can someone help understand why this happen?

Thanks

master-noddy commented 3 years ago

I got the same error, but I resolved it as my target file was not tab-separated. Please check your target file for the same.