Hello, What does the header from the "samtools view -bT $reference $file > $bamfile" bam file look like?
Regards, Andrew ________________________________________ From: Baiba Alksere <baiba.alks...@gmail.com> Sent: 02 September 2020 09:24:18 To: samtools-help@lists.sourceforge.net Subject: [Samtools-help] problems with header [EXT] Hello, I have a problem with samtools newest version and BWA tool from Sourceforge. I have sam files, but it looks like samtools are not recognizing header, and also not doing indexing. Is that a problem with bwa alignment, or samtools? scripts and samtools error message example are attached. -- 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. _______________________________________________ Samtools-help mailing list Samtools-help@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/samtools-help
