Unable to convert from sam to bam file.
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.
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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.
BWA Aligner.
Well, what does the header look like?
An empty file.
What do you get when you try
If you have an empty file they your alignment did not work. You will need to debug your
bwastep.Thanks I have did it and it works.
You might be using the samtools new version which has changed the input parameters. Which samtools version are you using?