What software tools can merge FASTQs and BAMs (SAMs) separately ?

Question

[flight22121]

What software tools can merge FASTQs and BAMs (SAMs) separately?

Tried only SAMTools for BAMs

[GenoMax]

you should be able to cat fastq files together on unix. Since you are working on Windows you may not have an easy native option for cat.
Merging two fastq files
merge large amount of fastq files into a single one

[Michael]

With windows 10 and its bash op could either use cat with that or https://stackoverflow.com/questions/60244/is-there-replacement-for-cat-on-windows .

Answer 1

[d-cameron]

Picard tools has a number of tools for merging SAM/BAM/CRAM including MergeSamFiles (samtools merge equivalent) as well as more specialised merging such as MergeBamAlignment and GatherBamFiles.