How can we get the germline single cell SNVs in my single cell data ?

Question

How can we get the germline single cell SNVs in my single cell data ?

Goatofmountain opened this issue 4 years ago · comments

Hello,
It seems that the vcf output file represents for the somatic SNVs of the single-cell WGS data only. How can I get all the SNVs including somatic and germline SNVs of single-cell data ?

Thank you

jluquette · Answer 1 · Thu May 14 2020 00:37:05 GMT+0800 (China Standard Time)

Hi,

Sorry for the late response. SCAN-SNV is currently only a somatic caller and does not call germline SNVs. If you'd simply like to get the list of germline sites, you can parse the GATK output yourself. The file is here: <scansnv_output>/gatk/hc_raw.mmq60.vcf.

I would start by extracting the column corresponding to your bulk input from that file and finishing the GATK best practices workflow by running VQSR. After the final germline calls are generated by VQSR, you could then return to the hc_raw.mmq60.vcf file to extract the germline sites for each single cell.

Hope this helps.