Show uncovered positions in pileup files

[SquirrelSeq]

Hello everyone,

I created pileup files from sam/bam files via Samtools.

For every reference in the alignment, the pileup entries start from the 5'-most reference position that is covered by reads.

How can I force Samtools to list the uncovered positions too?

Best regards,
SquirrelSeq

[SquirrelSeq]

I know that Samtools is very common in NGS data analysis.

So is my question confusing or not precise enough?

[mmanrique]

Hey, take a look at this thread

http://seqanswers.com/forums/showthread.php?p=98872

is this what you wanted to do?