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

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3.9 years ago

dongguiying2017 • 0

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 • 1.0k views

ADD COMMENT • link 3.9 years ago by dongguiying2017 • 0

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samtools quickcheck?

ADD REPLY • link 3.9 years ago by cpad0112 21k

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

ADD REPLY • link 3.9 years ago by dongguiying2017 • 0

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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.

ADD REPLY • link 3.9 years ago by GenoMax 141k

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