how to check the integrity of a sam file derived from bwa mem?
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17 months ago

Hi, I use the clusters to generate .sam files by bwa mem, but the clusters is closed when the sam files are generated. I have hundreds of sam files. Some sam files have been generated, and some are being generated. I want to know how to check the integrity of my sam files, except for checking their lastest modified times?

genome sequencing alignment • 462 views
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samtools quickcheck?

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I have tried samtools quickcheck. But even the sam file is not integrity, nothing are output

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If you suspect that some of your SAM files are incomplete then there is probably no other way but to check that you have at least the same number of fastq records in your files as the input data.

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