Samtools MPILEUP on single-end/paired-end data

Question

[christianhinze]

Hi everybody,

for variant calling, i am using samtools mpileup.

as far as i know, mpileup is by default ignoring certain reads (duplicate, failed QC, non-primary, unmapped).

my question, how is its default handling of single-end and paired-end data?

for paired-end data, i have the impression, it only accepts properly paired reads and ignores for instance singletons.

what about single-end data?

is it:

1. if it's paired-end data, pileup only properly paired + user defined (-q -Q) + no QC, no duplicates (default)...
2. if it's single-end, pileup only user defined (-q -Q) + no QC, no duplicates (default) ????

thanks, chris

[Brian Bushnell]

cross-posted:

http://seqanswers.com/forums/showthread.php?t=49253

[GouthamAtla]

The use of duplicates depends on marking the duplicates. So it depends on how you mark the duplicates before running mpileup. As far as I know, it should not ignore singleton reads.