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

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.

snp
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updated by Biostar Biostar • written by juncheng juncheng

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.

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written by Matt Shirley Matt Shirley

1 answer

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

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written by Devon Ryan Devon Ryan

Thanks you, again. :)

Indeed, the output of tophat is sorted.

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written by juncheng juncheng

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