Do I need to sort the .bam file for SNP calling by samtools?

Question

[juncheng]

Hi,

I'm running samtools for snp calling with human RNAseq data. Is it necessary to sort the tophat aligned bam file for snp calling?

I care about this because I have a lot of samples, sorting bam file means double amount of storing space needed.

Thanks.

[Matt Shirley]

Just as an FYI, you don't really need double the space - you can sort one or a few samples at a time and then delete the unsorted file. You won't need it as long as the sorted BAM is completely written.

Answer 1

[Devon Ryan]

Tophat will normally sort its output BAM files. Otherwise, yes, the BAM file would need to be coordinate sorted.

[juncheng]

Thanks you, again. :)

Indeed, the output of tophat is sorted.