I'm trying to get .vcf files from a .sam file via the following commands:
The sorted .bam file is ~130GB, and the final command I'm running seems like it will take forever to complete. It's been running for a couple of days, and the .raw.bcf file is only 85MB so far.
Is this normal? Is there an option in samtools/bcftools for multithreading, or am I doing something incorrectly?
Thanks!
Code:
samtools view -bt ${fai} ${prefix}.sam > ${prefix}_unsorted.bam samtools sort ${prefix}_unsorted.bam ${prefix} samtools mpileup -ugf ${fasta} ${prefix}.bam | bcftools view -bvcg -p - > ${prefix}.raw.bcf
Is this normal? Is there an option in samtools/bcftools for multithreading, or am I doing something incorrectly?
Thanks!
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