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Old 03-12-2012, 08:36 AM   #1
Location: Atlanta, US

Join Date: Jan 2010
Posts: 59
Default samtools sorting outfile is not as large as input file

I tried to sort a bam file for paired-end genomic data using samtools sort option. BAM file size is about 85gb. I sorted them on read names instead of chromosome coordinates. The output file is about 79gb. I am wondering where did 6gb of data from the input file go? Has anyone seen this type of inconsistency before?

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