Rsamtools and BAM file discordance

Question

[biomagician]

Hi,

I have this read in my BAM file. It maps on chromosome I.

I open this BAM file in IGV, and I can see the alignment on chromosome I.

But when I open this file in R with Rsamtools:

bamContigsCel <- Rsamtools::scanBam('output/alignment/pacbio/bwa/ref/bristolAssemblySorted.bam', param = Rsamtools::ScanBamParam(what = Rsamtools::scanBamWhat(), flag = Rsamtools::scanBamFlag(isMinusStrand = FALSE), tag = bamTags))[[1]]

I then check if the read maps to chromosome I in my R object but I cannot find it.

bamContigsCel$rname[bamContigsCel$qname == '000000F|arrow']
[1] II II IV
Levels: I II III IV MtDNA V X

But if I look at the BAM file, it's there. Why isn't Rsamtools importing my read into R?

samtools view bristolAssemblySorted.bam | grep -n '000000F' | head -c80
000000F|arrow   2064    I   336331  7   2926310H260M1774267H    *   0   0   GAAGCTGTCTAAACTTTGGC

Thanks. Best, C.

Answer 1

[Devon Ryan]

Cross-posted elsewhere where I already answered.