A bash + R script to plot the file size of BAMs vs. that of corresponding FASTQs to identify outliers where a BAM appears to have gotten truncated.

findbadbams.bash

cd /my/working/dir/
du -sb *.bam > bam.filesize  # two-column list of BAMs and their size in bytes
cat fastq.12col | awk '{print "du -sb "$1}' | bash > fastq.filesize  # two-column list of FASTQs and their size in bytes
# switch to R
R
fastq = read.table('fastq.filesize',header=FALSE)
bam = read.table('bam.filesize',header=FALSE)
bam$name = substr(bam$V2,1,21) # parse a unique ID for the BAMs from the path
fastq$name = substr(fastq$V2,71,91) # same for FASTQs
bam$bamsize=bam$V1 
fastq$fastqsize=fastq$V1
merged = merge(fastq,bam,"name")[,c("name","bamsize","fastqsize")]
dim(merged) # 192 3

# plot bam vs. fastq size without names
png('bam.vs.fastq.size.png',width=500,height=500)
plot(merged$bamsize,merged$fastqsize,pch=19)
dev.off()

# and with names to identify any outliers
png('bam.vs.fastq.size.with.labels.png',width=500,height=500)
plot(merged$bamsize,merged$fastqsize,pch=19)
text(merged$bamsize,merged$fastqsize,labels=merged$name,pos=4,cex=.8)
dev.off()

# write out results for later
write.table(merged,"merged.size.txt",sep="\t",col.names=TRUE,row.names=FALSE)

# browse a list of potentially bad BAMs
badbams = merged$name[merged$fastqsize/merged$bamsize > .41] # .41 is arbitrary cutoff from visual inspection of plots
badbams

q()
n