Try samtools mpileup -A -Q0 -f ucsc.hg19.fasta t.sam > t.pileup
On 6 April 2016 at 13:28, Daniel Chau <[email protected]> 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 > > > > ------------------------------------------------------------------------------ > > _______________________________________________ > Samtools-help mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/samtools-help > >
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