In a recent experiment with a few thousand barcoded cells I wanted to investigate common SNPs. I have a large .bam file consisting of all reads from all cells which passed quality control for which I have run variant calling and subsequent QC on the called variants - this was saved in
calls.vcf(the filtered vcf file contains ~70k sites).
I split my large bam file into one bam file per cell and also ran variant calling on individual cells using
calls.vcf as my regions file meaning I now have a large number of vcf files (one per cell) containing variant data on that cell in the specified regions. Using these vcf files I would like to construct a SNP-Cell matrix.
Is this possible using already released packages?