Hi folks,

When converted from a bam (5G) for a sample, the mpileup was too small (400K).

(>> samtools mpileup -BQ0 -d 1000000 -f hg19.fasta my_sorted.bam > my_sorted.bam.mpileup) <- this works for other samples.

BAM file was normally created by BWA.

I've checked a pile of reads in a region of the BAM but ZERO read counts in the mpileup.

I can't figure out why...

any suggestion?

thanks in advance.