BAFExtract for use of CaSpER, .snp or .baf?

[rhlgyb]

Hello,

I am using the BAFExtract for CaSpER to analyze single cell RNA-seq data.
On generating the baf values, the example says to run this following code :

mkdir test; samtools view SRR1295366.sorted.bam | ./bin/BAFExtract -generate_compressed_pileup_per_SAM stdin hg38.list test 50 0; ./bin/BAFExtract -get_SNVs_per_pileup hg38.list test ./hg38/ 20 4 0.1 test.snp

My question is, should the <output_baf_file> be test.snp as above or test.baf?

Thanks a lot!

beemilmlo

[arjun0502]

@beemilmlo Did you figure this out?

[rhlgyb]

I’ve been looking around some of the other codes and posted materials and decided to go with .snp .
The results for .snp and .baf were the same when I tested both codes on my data.