Question: Trouble With Kb1454Chr5.Bam, Bushman Chrm5, 454 Data Only
0
Allan Lindh • 10 wrote:
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,
except
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
Chromosomes.
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.