Large Bam, But Small Mpileup (Samtools Mpileup)

Question

[gen]

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.

[Devon Ryan]

Does it look fine under igv or another viewer?

BTW, why is this listed as a tool?

Answer 1

[always_learning]

Similar discussion were made at http://seqanswers.com/forums/showthread.php?t=24132