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freeseek / mocha

MOsaic CHromosomal Alterations (MoChA) caller
MIT License
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GC content in VCF file #35

Closed AkshajD closed 1 year ago

AkshajD commented 1 year ago

Forgive me for the naïve question, but I am new to genetic analysis and struggling with one of the requirements of this pipeline.

I have WGS data in BAM formats that I am currently running through GATK's HaplotypeCaller in order to get the VCF file. However, upon inspection of this file, while I have all the other requirements, I don't seem to have the GC content.

I have tried searching it up online but wasn't able to find any information on this. As I understand, the original, unphased VCF file that runs through the remainder of your tutorial should have this information, so do you have any recommendations?

freeseek commented 1 year ago

You can add the INFO/GC field with the command

bcftools +mochatools --no-version -Ob $vcf -- -t GC -f $ref
AkshajD commented 1 year ago

Perfect, that worked!