Samtools - huge mpileup file!
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9.2 years ago
lcc1844 ▴ 40

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!

alignment next-gen • 5.5k views
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Use pipe...

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We're in the pipe five by five:

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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!

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Pipes are your friend: zcat file.vcf.gz | less.

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9.2 years ago

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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Thanks very much, I ran the command you suggested and it took many hours and generated a zipped .vcf file that is 21GB. Is this not larger that what I could expect from one human exome?

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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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