diff --git a/R/plot_GATK_performance_log.R b/R/plot_GATK_performance_log.R
index f63768b14..39b2b3c70 100644
--- a/R/plot_GATK_performance_log.R
+++ b/R/plot_GATK_performance_log.R
@@ -6,6 +6,8 @@ DATA_FILE = args[1]
 DESCRIPTION = args[2]
 OUTPUT_PDF = paste(DATA_FILE, ".pdf", sep="")
 
+MAX_POINTS = 1000
+
 if ( onCMDLine ) { 
    print(paste("Reading data from", DATA_FILE))
    d = read.table(DATA_FILE, header=T)
@@ -19,6 +21,15 @@ vec.margin <- function(x) {
     c(x[1], d[1:(l-1)])
 }
 
+everyNth <- function(x, n) {
+    l = dim(x)[1]
+    m = ceiling(l / n)
+    print(m)
+    keep = 1:l %% m == 0
+    x[keep,]
+}
+
+
 l = length(d$units.processed)
 d$units.processed.margin = vec.margin(d$units.processed)
 #prev = 0
@@ -32,14 +43,15 @@ generateOneReport <- function(d) {
     qs = quantile(d$processing.speed, probs = c(0.01, 0.5, 0.99))
 
     # unit processing time
-    plot(d$elapsed.time, d$processing.speed, main=DESCRIPTION, xlab="Elapsed time (sec)", ylab="Processing speed (seconds per 1M units)", ylim=c(qs[1], qs[3]), type="b", col="cornflowerblue", lwd=2)
+    dpoints = everyNth(d, MAX_POINTS)
+    plot(dpoints$elapsed.time, dpoints$processing.speed, main=DESCRIPTION, xlab="Elapsed time (sec)", ylab="Processing speed (seconds per 1M units)", ylim=c(qs[1], qs[3]), type="b", col="cornflowerblue", lwd=2)
     abline(h=qs[2], lty=2)
 
     # instantaneous processing speed
     running_median_window = 101
     rm = runmed(d$units.processed.margin, running_median_window)
     POINT_COL = "#0000AA33"
-    plot(d$elapsed.time, d$units.processed.margin, main=DESCRIPTION, xlab="Elapsed time (sec)", ylab="Units processed in last timing interval", type="p", cex = 0.5, col=POINT_COL)
+    plot(dpoints$elapsed.time, dpoints$units.processed.margin, main=DESCRIPTION, xlab="Elapsed time (sec)", ylab="Units processed in last timing interval", type="p", cex = 0.5, col=POINT_COL)
     lines(d$elapsed.time, rm, lwd=3, col="red")
     legend("topleft", c("Observations", "101-elt running median"), fill=c(POINT_COL, "red"))
 }