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griffithlab / neoag_protocol

Protocol for end-to-end neoantigen analysis and vaccine design for a single patient
MIT License
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Run Germline Exome and HLA typing workflow #4

Open jhundal opened 4 years ago

jhundal commented 4 years ago

Replicate the Germline Exome & HLA typing stepwise on AWS and record documentation on Google doc.

ssupabphol commented 4 years ago

I reach the final step of this part (optitype). Unfortunately, the file sizes are not equal to those from brca_example in compute0. Bryan said the reason is due to previous incomplete optional references. So I will rerun the whole section again with the same commands.

ssupabphol commented 4 years ago

After reruning with optional references, new bam files are equal to those from brca_example (checked by samtools flagstat).

ssupabphol commented 4 years ago

Unfortunately, qc_exome part got the unmatched output files. At this time, I will just skip this part.

ssupabphol commented 4 years ago

All bam, cram files, and optitype outputs are equal. VCF and some QC files are not equal. VCF files are a bit different even though I double checked input arguments with Bryan already. I wonder if the difference between vcf files might be due to updated "germline_detect_variants.cwl".