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jonahcullen / wags

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Using prep_custom_ref.py #34

Closed sachin-subedi closed 1 year ago

sachin-subedi commented 1 year ago

Hi Dr. Cullen

I have downloaded the SRA files of dogs from NCBI and converted them into FASTQ format using the SRA toolkit in the cluster. I am trying to use WAGS to align them to CanFam4 to get output in gvcf, which I will later combine into gvcf files. I am going through the paper on WAGS as well as Git Hub. I am trying to use prep_custom_ref.py to convert FASTQ to BAM. Can “prep_custom_ref.py” work for this?

Best, Sachin

jonahcullen commented 1 year ago

So prep_custom-ref.py would be used if you wanted to use a difference canine reference that is not in the container. If you want to process FASTQ to BAM and to GVCF, you'll want to checkout prep_subs.py. Try running python prep_subs.py --help to see the available options (for example --ref can be used to specify canfam4 or UU_Cfam_GSD_1.0_ROSY which is canfam4 + chrY.

sachin-subedi commented 1 year ago

Thank you Dr.Cullen