Estimate of BAI size relative to BAM size

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2.7 years ago

joshua.theisen ▴ 30

Is there a rule of thumb for how large a BAI file will be relative to a BAM file? For example, if I have a BAM file that is 1GB and a supposed companion BAI file that is 1GB, would this be suspicious? What if the BAM is 1GB and the BAI is 1MB? Thanks.

bai bam • 849 views

ADD COMMENT • link updated 2.7 years ago by ATpoint 85k • written 2.7 years ago by joshua.theisen ▴ 30

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Rule of thumb in my experience that the index is roughly the size of the BAM in Gigabyte divided by 1000, so like 1GB BAM makes a 1MB index. Very very roughly...

Yes, a 1GB index for a 1GB BAM is suspicious.

ADD REPLY • link 2.7 years ago by ATpoint 85k

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~1:1000 is what I was expecting. Not sure why my BAI is the same size (~2GB) as my BAM. Thanks!

ADD REPLY • link 2.7 years ago by joshua.theisen ▴ 30

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You can check by renaming it into .bam and run samtools view, if a proper SAM files comes out then probably some stdout stream got caught up incorrectly.

ADD REPLY • link 2.7 years ago by ATpoint 85k

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