de novo variant SNP calling from barcoded single-cell data

Question

[dominicdhall]

I have a BAM file containing sorted, aligned reads from a number of single cells. Each read has an associated cell barcode (CB tag). I would like to consider all aligned reads and produce a VCF file of SNP variants from my single cell data. I have looked over the documentation for bcftools mpileup and found useful options such as --ignore-RG to ignore the readgroup when assigning a genotype probability. I therefore wanted to run something like:

bcftools mpileup -Ou --ignore-RG --no-reference -b <input.bam> | bcftools call -mv -Oz -o calls.vcf

My question is: will mpileup group reads by barcode when calculating genotype probability? Will this method successfully output SNP variants present within my aligned reads?

[swbarnes2]

Are you sure you have enough depth do to variant calling?

[dominicdhall]

I didn't produce the data set but I have been assured that there is the necessary depth to work out a sample of variant SNPs present within each cell.

Answer 1

[niklas.lang]

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