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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.

benson23
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khanhlpbao
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  • Stack Overflow is for specific programming questions. It's unclear from your question what exactly you are doing. You should some minimal code or provide a [reproducible example](https://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example) to make it possible to help you. All necessary info should be in the question itself and not linked externally. But given the nature of the data and subject area, maybe this is a better fit for [bioinformatics.se] rather than Stack Overflow. – MrFlick Apr 22 '21 at 02:55
  • @MrFlick thank you, I will ask on Bioinformatics. About reproducible example the file is so large (about 1-1.5gb) so I cannot post it on here. – khanhlpbao Apr 22 '21 at 03:34

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