Re: [Samtools-help] A question about "mpileup"

[David Jones]

Hi Daniel, Looking at the reads in the attached sam file you have only 4 reads marked as ‘properly paired’. You can establish this by looking at the values in the FLAG field for each read.  By default mpileup excludes these ‘anomalous’ (not properly paired) reads. If you to add -A to your command you would see all of the reads are included in the pileup (see attached). samtools mpileup -Q0 -A t.sam > t2.pileup David Jones d...@sanger.ac.uk Principal Bioinformatician Cancer Genome Project (Team 78) Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SA UK -- The Wellcome Trust 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.

t2.pileup
Description: Binary data

On 6 Apr 2016, at 06:28, Daniel Chau <danicha...@gmail.com> wrote: Hello everyone, I am an undergrad and newbie to bioinformatics. Recently I encountered a problem that I could not solve on myself. A pileup file was generated by this command: samtools mpileup -Q0 -f ucsc.hg19.fasta t.sam > t.pileup . There are 9 alignment items in that sam file, but only 4 of them are shown in the pileup file. Both the sam file and the pileup file are attached. Sum of them are smaller than 1MB. I really hope you could help me and tell me why whose 5 alignment items are abandoned by samtools. Sincere appreciation. Daniel Chau <t.pileup><t.sam>------------------------------------------------------------------------------ _______________________________________________ Samtools-help mailing list Samtools-help@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/samtools-help

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