I'm trying to study fetal fraction by using a seqff script from here.
The instruction says that I need a headless sam file to work so after alignment with bwa
, I process my sam file by using samtools
:
samtools view -S -q 20 target.sam > treated.sam
This process also remove the @SG header since there is no reference file. I also use grep
to remove header of the target.sam got after alignment for comparison. However, when I compare, I noticed that ENet calculation on the treated.sam returned with NA results, so half of the method to calculate fetal fraction of this script was gone.
I have tested it in multiple cases and it seems that without using samtools
, the script worked well but with samtools
Enet calculaton not worked. Can someone tell me what is wrong with the script?
I'm using R 4.0 and all modification I made to the script is on the args since it cannot recognize args I input with anymore.