Free software to analyze circulating tumor DNA?

[ymc]

Metastatic cancer patients usually have traces of tumor cells in their blood. I heard that people are beginning to check the DNA of these tumor cells in blood to monitor the cancer mutation process.

Is there a free software that can find SNPs of these tumor DNA? I suppose such software will also work for fetal DNA in maternal blood.

Thanks in advance!

[james hadfield]

The Forshew e al paper has details of the analysis they used for ctDNA analysis with Fluidigm. I think it is the same as any other mutation calling.

[ymc]

Why do you say it is the same as other mutation calling? Supposedly, these tumor DNAs are mixed with the germline DNA from white blood cells. Their quantity is likely to be lower than the latter which makes them not suitable for typical SNP caller like GATK

A similar case will be fetus DNA in maternal blood. Is there any free software in that area, too?