Hi !

I am trying to generate a consensus .fastq sequence of my reads with Samtools pileup command from a .bam file generated by MosaikText (alignment software). So far, I tried :

$ samtools pileup -cf referenceseq.fa alignmentfile.bam ! samtools.pl pileup2fq -D100 > consensus.fastq

I was expecting to get something like this : @chrX nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnatgggtcccatacacacacgtgatgctataagtgtac tgatcatgtaccatgttagtactannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnttgatgcacacttttac gtttagtatcggataaatgtaccacacacatgtgggggtagtacagtnnnnnnnnnnnnnnnnnnnnnnnnn nnnnnnnnnnnnnnnnn etc.

But I get thsi : @chX nnannnnggnnnnnnnnnnnnncnnnnnnnnnctnnnnnnnnnannncnnnnnnnnnnnnnnnnnnnctnnn nnnnnnngnnnnnnnnnnnnnnnactnnnnnnnnnnnnnnnnnnnnnnntgnnnnnnnnnnnnnnnnnnnnn nnnnnnnnnnatnnnnnnnnnnnnnnnnnnnctnnnnnnnn etc. which is completly wrong.

I do not find where I did an error. Have somebody already been confronted to such a problem? Do maybe someone know how to do it differently out of a bam file?

Thank you very much! Lena