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lnscan / mitoSplitter

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running without bulk bam #3

Open isadeghi87 opened 9 months ago

isadeghi87 commented 9 months ago

Hi, I have a only pooled.bam, barcode and a vcf file which doesn't have mitochondrial variants. How can I run this in my situation?

best iman

lnscan commented 9 months ago

Hi, iman. I would like to know how your VCF file was generated. Are you able to calculate the mitochondrial allele frequency for each sample using other methods? If not, you may need to consider alternative demultiplexing methods. Because autosomes and mitochondria have different ploidy levels and the sequences are much longer, I do not recommend applying the mitoSplitter workflow directly to autosomal data.

best Lin

isadeghi87 commented 9 months ago

@lnscan So, If I have the vcf file from MT chromosome and the bam file including MT reads, can I run it?

lnscan commented 9 months ago

Indeed, if you are able to extract MT SNPs along with their allele frequencies from a VCF file like this: sample1 sample2 sample3 1_A 0.013779527559055118 0.018469656992084433 0.023668639053254437 1_C 0.007874015748031496 0.013192612137203167 0.007889546351084813 2_T 0.001968503937007874 0.0079155672823219 0.005917159763313609