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Old 04-28-2011, 11:14 PM   #1
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Location: St. Louis, MO

Join Date: Apr 2011
Posts: 4
Question sites missing from mpileup

I ran the following command thinking that it would return information for every site in my reference sequence (a transcriptome).

samtools mpileup -uf Ref.fasta aln.sorted.bam | bcftools view -bcg - > aln.sorted.bcf

However, ~2% of the sites are missing from the output. I wrote a perl script to determine which sites were missing and ~92% of the missing sites were from transcript ends. I guessed that perhaps sites that had no coverage were not returned; however, some internal sites with no coverage were returned. I have rulled out BAQ as being the problem as well as the same sites are consistently missing whether or not a BAQ calculation is used.

Does anyone know what would cause some of the sites to not be included in the output?

Thanks for your help!
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