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single-cell-genetics / cellsnp-lite

Efficient genotyping bi-allelic SNPs on single cells
https://cellsnp-lite.readthedocs.io
Apache License 2.0
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Understand AD matrix #18

Closed Zepeng-Mu closed 3 years ago

Zepeng-Mu commented 3 years ago

Hi,

I noticed the output sparse matrix AD.mtx contains only one value, but typically the AD filed in VCF file is a vector of two for bi-allelic loci. So I'm wondering what the number in the mtx file represent?

Thanks!

hxj5 commented 3 years ago

Hi, the AD.mtx contains the allele depths of the alternative (ALT) alleles while the DP.mtx stores the sum of allele depths of the reference and alternative alleles (REF + ALT). And the OTH.mtx contains the sum of allele depths of all the alleles other than REF and ALT.

Zepeng-Mu commented 3 years ago

Thanks!