[Samtools-help] Samtools mpileup leaving blanks in multisample

[Jesse R. <jes...@u2...>]

Hi, 
when I run mpileup

samtools mpileup -q 1 -B -f hg19.fasta 1.bam 2.bam > mpileup
I get some lines with missing data: 

chr1	13975	A	0	*	*	3	,,,	444
chr1	13976	G	0	*	*	4	,$,$,$.	000:
chr1	13977	T	0	*	*	0		
chr1	13978	C	0	*	*	1	.	4
chr1	13979	A	0	*	*	0		
chr1	13980	T	0	*	*	0		
chr1	13981	T	0	*	*	0		
chr1	13982	C	0	*	*	1	.	:

that then throws an error in VarScan


Version: 0.1.18-dev

thanks,