Sorry to bother you with this, but I am trying to process the KB1 Bushman
data, through a pipeline that starts with
samtools mpileup -C50 -uf ~/Bushman/hg18/chromFa/chr1.fa
../KB1illumChr1.bam ../KB1454chr1.bam | bcftools view -c -

Processing the data one cromosome at a time, aligning the data against
hg18, using mpileup to combine the illumina and 454 data.

All goes very well, everything looks good all the way through, results are
stable, hi-quality, and conceivably even meaningful,
for KB1454chr5.bam, the 454 data for Chrm5
When combined with the illumina data for Chrm5 it results in garbage, even
though if I run the illumina data alone, it looks like all the other

I confess that I am worse than a Newbie, I'm an old guy working on my own,
so may in fact just be in way over my head.  But if there is any chance you
could take a look at
KB1454chr5.bam to see if there were a lot of bad reads, or an error was
made in processing, or anything else is wrong, I'd be most grateful.
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