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Old 12-18-2012, 08:43 PM   #1
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Default extremely large vcf file generated using sam tools


This is my first time to Samtools. I tried to create .vcf files for my bam files of my paired-end RNA seq samples. I used

samtools mpileup -D -B -Q 20 -u -f /WholeGenomeFasta/genome.fa Sample.bam | bcftools view -gc - > Sample_positions.vcf
But for ~4GB of bam file it is creating(still running) ~ 75GB size of vcf file.

Is this normal or am I making a mistake some where?

Thanks in advance.

Last edited by janaahan13; 12-18-2012 at 08:46 PM.
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rna seq, sam tools, vcf

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