Variant callers for single cell WGS

Question

[Binny]

Which variant callers can be used for the detection of indels, SNPs, and CNVs in single-cell whole genome sequencing, where the sequencing was done using Illumina NovaX ?

Answer 1

[swbarnes2]

Of course you can run a cell ranger generated bam through a variant calling program or pipeline, but single cell sequencing is so spotty, and often biased to one end or the other of the transcript, you are going to miss a lot.

[GenoMax]

you can run a cell ranger generated bam

AFAIK 10x does not have a whole genome sequencing product for single cells so cellranger may not apply.

Binny : What technology are you using for this? This is the second time someone has asked about WGS in single cells and I am curious.

[Binny]

We use the MDA method to amplify the DNA. Library prep : DNA fragmentation - Repair - adaptor Ligation - size selection- pcr (optional) - purification