Hi all,
I am working with a single-cell RNA-seq experiment where two cell lines, HT29 (COAD) and KP4 (Pancreas), were multiplexed together before sequencing. The data has been aligned to the GRCh38 reference genome, and now I need genotype information to run demuxlet for sample demultiplexing.
I am looking for VCF (or compatible genotype files from which I can generate VCF) for these two cell lines.
What I found are: WGS (but from the sole HT29, not KP4) here and HC for both HT29 and KP4 (but unfortunately, based on this info, it looks that the HC files were generated from HG19).
Alternatively, I was thinking of one of the following files: OmicsSomaticMutationsMAFProfile.maf and
OmicsSomaticMutationsProfile.csv (the latter being a MAF-like file and not MAF, therefore perhaps less conveniently convertable to VCF).
I would greatly appreciate any suggestion to solve this problem.
Thank you so much!!
Luca
2 posts - 2 participants