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
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