I am a beginner in ngs bioinformatic analysis. I try to create a multisampled .vcf file from 250 .bam file using mpileup bcftools. Here the command I use:
bcftools mpileup -O z -o output.vcf.gz -f ref_genome.fasta bam_file_list*.bam
There are two questions I want to ask about this.
I use Linux machine with 32GB of memory, but only 10% of RAM being used by the system. Is there any way to increase the memory usage in the bcftools command line?
Can we show the expected time or progress bar in the bcftools command line? I was tried to insert
bcftools mpileup -O z -o output.vcf.gz -f ref_genome.fasta bam_file_list*.bam | pv -p -t -e but the time and bar didn't visualized the progress.
I hope you can help me to solve my problems.