Hi,
samtools mpileup does not generate data in the SAM format, so the files
produced by it cannot be read back by samtools view.
You can read more about the Pileup format
here<http://www.htslib.org/doc/samtools-mpileup.html#Pileup_Format>.
Anyway, what is your use case?
From: Baiba Alksere <baiba.alks...@gmail.com>
Sent: 27 October 2020 22:12
To: samtools-help@lists.sourceforge.net
Subject: [Samtools-help] generating headers [EXT]
Hello, Samtools Mpileup does not generate correct headers
After running samtools mpileup -A -E -f $reference $INPATH/*.bam > piled
I get ASCII file with no header
When trying to run downstream applications, like Lofreq, (and view header with
samtools view), I get error like "fail to read the header of file.bam"
Headers in my sam and bam files are correct
--
Best regards
Baiba Alkšere
--
The Wellcome Sanger Institute is operated by Genome Research
Limited, a charity registered in England with number 1021457 and a
company registered in England with number 2742969, whose registered
office is 215 Euston Road, London, NW1 2BE.
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