Samtools BAM to bcf question

[Phantom123]

Dear All,
i am using the following command to convert a BAM file to a bcf file:

samtools mpileup -uf genome.fa raw.accepted_hits.bam|bcftools view -bvcg - > raw.bcf

i think there is a way to insert the genome.fa.fai file (if it is available) in the above command to speed up the process of bcf file creation. does someone know how that is done?


Thanks for your help.

[swbarnes2]

The fai file is required for mpileup to work. If it doesn't find one, it will attempt to make it on the fly. So your command line is fine.

[Phantom123]

thank you.