I have a .bam file which contains exome capture data and is 10GB.
I used the following command to make an mpileup:
samtools mpileup -E -uf hg19.fa file.art.bam > file.mpileup
It took several hours of making the mpileup file and it got to over 100GB in size and my computer ran out of storage! So i obviously stopped this command running to start again. Why was the pileup so large?
My intention upon getting the mpileup file was to do variant calling using:
bcftools view -cg file.mpileup > file.vcf
Are these the right options for me?