About phased.vcf.gz generation during germline calling

[scg-dgist]

When I conducted the germline calling process, I noticed that only a limited number of chromosomes were successfully processed into 'phased.vcf.gz,' whereas most of the chromosomes remained unprocessed. I included all standard chromosomes (chromosomes 1-22) as listed in 'region.lst' and utilized the GRCh38 human reference FASTA file for this analysis. Could this variation in success be linked to the inherent low read depth typically associated with 10x scRNA-seq data? Additionally, I'm interested in knowing if there are any potential solutions to address this issue.

Many thanks.