CfDNA exercise answers

Q1

Using:

samtools stat /data/shared/exercises/cfdna/patient_1.bam > patient1.stat
samtools stat /data/shared/exercises/cfdna/patient_2.bam > patient2.stat

plot-bamstats -p patient1 patient1.stat
plot-bamstats -p patient2 patient2.stat

firefox patient1.stat
firefox patient2.stat

Both peak at 168bp however patient 1) clearly has the greatest variance and has an overabundance of short DNA fragments compared to patient 2.

Q2

We first run:

readCounter --window 100000 -c 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22 /data/shared/exercises/cfdna/patient_1.bam > patient_1.wig 
readCounter --window 100000 -c 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22 /data/shared/exercises/cfdna/patient_2.bam > patient_2.wig 

to get the fragment counts per 100kb window. Then:

grep -v fixed patient_1.wig  |wc -l 
28823

Q3

Running:

/data/shared/exercises/cfdna/plotCNV.R patient_1.wig 
/data/shared/exercises/cfdna/plotCNV.R patient_2.wig 
evince patient_1_CNV.pdf
evince patient_2_CNV.pdf

Clearly shows that patient number one has a lot of alterations in terms of copy number.

Q4

Based on the plots for the fragment size distribution and copy number variations, patient 1 had lung squamous cell carcinoma and patient 2 was a healthy control.