Closed hyunhwan-bcm closed 1 month ago
Hi, @hyunhwan-bcm can you also review the other options listed here: https://chatgpt.com/share/43eb88c5-9850-49a7-a0db-793289daea0f
I think it would be great if we can use vcftools or bcftools options so we don't need to install, and it does not require us to get reference files.
Sorry but I am in difficulty at understanding the meaning of Taks2 and Task3.
It seems the task2 already incorporated some logics of VCF_PRE_PROCESS
, but there is something missed too.
bcftools annotate --rename-chrs ...
commandbcftools annotate --set-id +'%CHROM\\_%POS\\_%REF\\_%FIRST_ALT'
commandbcftools filter ${params.run_id}-add-id.vcf.gz -i'FILTER == "PASS"'
Is it intended as they are already covered by new commands? or just mistakes by ChatGPT?
This needs to be executed before VCF_PRE_PROCESS, and bcftools annotate --rename-chrs
is required to drastically reduce many non-variant records. After that, we will proceed with the other two parts.
The gVCF to VCF conversion logic will be added to the VCF_PRE_PROCESS stage.
Then this is irrelevant, and safe to be ignored, right?
Would you like to make any modifications or additions to this draft before posting it?