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?
Thank you!
1 answer
A pileup file is text-based, so it's going to be large. Assuming you have the most recent version of samtools, just use samtools mpileup -Euvf hg19.fa file.art.bam | bgzip > file.vcf.gz.
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written
by
Devon Ryan
It seems rather large to me, but you could just look at the results to see if they make any sense.
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written
by
Devon Ryan
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Use pipe...
We're in the pipe five by five:
I stopped unzipping the file because my computer ran out of space. I must have done something wrong somewhere because the .vcf should surely be much smaller than fastq and bam!
Pipes are your friend:
zcat file.vcf.gz | less.