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.
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.
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