Picard CalculateHsMetrics Function - what do all the output abbreviations mean?

[gwilymh]

Hi,

I am using the CalculateHsMetrics in Picard to estimate the per cent of on and off target reads for some next generation sequence data that I am aligning against a reference genome. I am running Picard via the Galaxy server (usegalaxy.org/).

I am having trouble understanding some of the program outputs. A list of my specific queries is given below. Any advice anyone can give me would be greatly appreciated.


What do the following outputs stand for?
PF_READS
PF_UQ_READS_ALIGNED 5403054
PCT_PF_UQ_READS_ALIGNED
PF_UQ_BASES_ALIGNED
ON_BAIT_BASES
ON_BAIT_VS_SELECTED
FOLD_ENRICHMENT
ZERO_CVG_TARGETS_PCT
FOLD_80_BASE_PENALTY
HS_PENALTY

I am also unsure about exactly what these outputs refer to:
BAIT_TERRITORY and TARGET_TERRITORY - are these references to the total number of base pairs captured by the baits and targets?
NEAR_BAIT_BASES - how near the baits are these bases? I understand that they cover a 250bp interval around each target or bait. Is this what the output is referring to?
PCT_SELECTED_BASES - does this refer to the percent of the referene genome captured by the targets or baits?
OFF_BAIT_BASES vs NEAR_BAIT_BASES - does the count of off-target bases include those bases that are near the baits/targets?

[ersgupta]

refer to this page http://picard.sourceforge.net/picard...html#HsMetrics

[gwilymh]

Thank you ersgupta, much appreciated.