smoove call for tumor/normal pairs

[TLyan-ze]

Hi, I want to make sure that when I use smoove call for tumor/normal pairs.
Is there a requirement for the order of two bam files?
Which command is correct ?
The command is as follows:
smoove call -x --name sample --fasta genome.fa -p 4 --genotype --outdir ./ path/normal.bam path/tumor.bam
smoove call -x --name sample --fasta genome.fa -p 4 --genotype --outdir ./ path/tumor.bam path/normal.bam

Thanks in advance!

[brentp]

Hi, the order doesn't matter. You'll have to decide post-hoc what is somatic and what is not (the genotypes won't help you there as they are for diploid samples).

[TLyan-ze]

ok, thanks!