error in getBamCounts:[samopen] no @SQ lines in the header

[jeetendra-kuld]

Hi vplgnol
Thanks for this wonderful tool. we are trying to setup CNV pipeline for germline samples, but we are facing some issue mentioned below. Can you please look into the issue and let us know the solution. This would really help us to accelerate in setting up our pipeline.

1. R version is 3.6.3
2. samtools = Version: 1.9 (using htslib 1.9)
3. bwa = Version: 0.7.12-r1039

thanks alot

my.counts <- getBamCounts(bed.frame = exons.hg19, bam.files = "bams.list", include.chr = TRUE)
Parse 1 BAM files
[1] "bams.list"
Now parsing bams.list
[samopen] no @sq lines in the header.
Error in value[3L] :
failed to open BamFile: SAM/BAM header missing or empty
file: 'bams.list'