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 -
Chrm1_illum_454.vcf
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.