Error on somatic calling

[solarkang21]

Hello, thank you for a great tool!

I have successfully(maybe?) finished the preprocessing and germline calling step thanks to your kind tutorials. However, I need some help with somatic SNV calling step.

With multiple snRNA-seq samples, I got one filter.bam.lst for each chromosomes in the preprocessing step. Then I ran the germline calling step with GRCh38.region.lst, provided file in Monopogen/resource, getting one or more vcf/phased.vcf.gz/gl.vcf.gz files for each chromosomes. (e.g. chr1:1-50000001.germline.vcf, chr1:50000001-100000001.germline.vcf ...)

This is where I face a problem. When I use the region.lst that matches the germline outputs(e.g. chr1:1-50000001) for somatic SNV calling step(featureInfo), it says: AssertionError: The bam list file {path}/preprocess/Bam/chr1:1-50000001.filter.bam.lst cannot be found!

So when I change my region.lst to only contain chromosome numbers(e.g. chr1 \ chr2 \ ...), it says: AssertionError: The *.gl.vcf.gz file {path}/preprocess/germline/chr1.gl.vcf.gz cannot be found! Please run germline module

So my question is, Is the germline SNV calling step supposed to return one gl.vcf.gz files even if I use the provided region.lst file? If not, am I supposed to run germline SNV calling step with region list only with chromosome numbers(e.g. chr1 \ chr2 ...)?

Thank you in advance for your consideration.

[solarkang21]

I got through it, thanks!