Hi!
I have three aligned pair end reads in BAM format. Two of them are of same sample run in different lanes. I first merged the files from same sample with read groups and added read group to third one separately. After that I merge all three bam files into one, also changing header to required one. I then tried to sort the merged bam file. But this is what I get as a sorted file. File_RG.sorted.0000.bam , File_RG.sorted.0001.bam, File_RG.sorted.0002.bam and so on....
Why am I not able to sort the BAM file? I am using samtools for merging and sorting.
Are you waiting for the command to finish, or is it crashing early for some reason? samtools sort will make those intermediate files (0000, 0001, etc.) since it cannot hold all reads in memory during the sort. It will do a final mergesort that produces the single bam you want, and should then delete those intermediate files.
You don't even need to delete them, they are merged back to the output file prefix you gave, while launching the command.
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