sorting of BAM files #39
Description
Hi!
I'm currently using the accuMUlate tool on my samples, but I have faced one weird error when the job finishes.
I receive several times the message "Pileup::Run() : Data not sorted correctly!".
Nonetheless I have the accuMUlate output as .txt and it is reasonable.
According to samtools, it was sorted and everything appears to be right with the merged bam file (20 bams in total).
Was this problem already reported and can it interfere on the output? Should the merged bam file be sorted? (since it was reported that for large datasets it sometimes doesn't work)
My pipeline was:
picard MergeSamFiles to merge; followed by samtools sort and samtools index.
I would appreciate your input on this unusual error.
Thank you