Unable to convert from sam to bam file.

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2.9 years ago

usef • 0

samtools view -S -b BD143_TGACCA_L005.sam -o BD143_TGACCA_L005.bam

When I am running this command the following error is appearing:

[main_samview] fail to read the header from "BD143_TGACCA_L005.sam"

As a result, if anyone knows how to fix this error and thanks.

bam sam samtools • 1.7k views

ADD COMMENT • link updated 20 months ago by Ram 44k • written 2.9 years ago by usef • 0

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Which aligner did you use to generate the SAM file? All aligners should write a valid header when the originally create that file.

ADD REPLY • link 2.9 years ago by GenoMax 147k

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BWA Aligner.

ADD REPLY • link 2.9 years ago by usef • 0

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Well, what does the header look like?

ADD REPLY • link 2.9 years ago by swbarnes2 14k

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An empty file.

ADD REPLY • link 2.9 years ago by usef • 0

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What do you get when you try

head -3 BD143_TGACCA_L005.sam

If you have an empty file they your alignment did not work. You will need to debug your bwa step.

ADD REPLY • link 2.9 years ago by GenoMax 147k

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Thanks I have did it and it works.

ADD REPLY • link 2.9 years ago by usef • 0

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You might be using the samtools new version which has changed the input parameters. Which samtools version are you using?

ADD REPLY • link 2.9 years ago by Roger • 0

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