Dear all,
I have searched Rsamtools help pages and the mailing lists archives, but I
couldn't find an answer to my question: is there any function to write a
BAM file from within R?
I use the scanBam function to read in R an input file and, after some
merging and filtering within R, I would like to write the output a BAM file.

Have you any suggestion? My first option at the moment is to create a SAM
text file by writing the fields in the corresponding order and then use
samtools to convert the SAM in BAM, but maybe there is a better solution
that I have missed.

Thank you all in advance.

Best,

Margherita

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