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4.1 years ago
In order to use genomic data in IGV I converted SAM files to BAM and them executed the index via samtools. I observed that when generating the index from the same BAM file the output could have different sizes. To test I inputed the same genome three times, with diferent index in IGV and verified slighth diferences as shown in the image. Does anyone knows if i have done something wrong, or if that is a normal thing? Thanks in advance!
Size of files is never a good criteria to judge validity of a command/action. If IGV is not complaining about the indexes then they are fine.
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Thank you for your help! I can't understand why, when using the same input file and the same command, the size of the output can be different. That´s messing with my head. Do you know the reason why this happens?
Can you show us what kind of difference are we looking at? Many NGS data analysis program produce "non-deterministic" output (i.e you may get slightly different results each time you run a dataset). In practice this is not a big problem. Some of the programs will allow you to set a
seedso you get exactly the same result each time. I don't know ifsamtools indexis one of those operations.Thank you, once again, for your help! I am really sorry but my question was the result of a mistake, that i only realysed now. I was using the computer at distance, i don't know if it was some kind of delay but the truth is that now i'm looking at the same files at the computer and they do have the exact same size! I'm really sorry! Thank you once again!