search

diskin-lab-chop / AutoGVP

19 stars 3 forks source link

modified dockerfile to install bcftools #56

Closed naqvia closed 1 year ago

naqvia commented 1 year ago

Modify Dockerfile to install bcftools

naqvia commented 1 year ago

I used that example above and what we had on cavatica (bix tools). But it seems they do not working bc the paths do not exist anymore. The latest Dockerfile works and has been built and pushed.

naqvia commented 1 year ago

I have tested it and it runs. Here are a few examples:

bcftools filter -i 'INFO/AF <=0.01' input/6836213c-dbe1-48b4-9a66-55dcc25ec024.single.vqsr.filtered.vep_105.vcf.gz
bcftools filter -i 'INFO/gnomad_3_1_1_AF_popmax <=0.01' input/6836213c-dbe1-48b4-9a66-55dcc25ec024.single.vqsr.filtered.vep_105.vcf.gz
bcftools filter -i 'INFO/DP >=100' input/6836213c-dbe1-48b4-9a66-55dcc25ec024.single.vqsr.filtered.vep_105.vcf.gz

These expressions need to be defined in the vcf header. Below is an example of when it fails I suggest this is done by the user and then the filtered vcf is ran through the tool.

naqvia commented 1 year ago

Got it to install specific version and also added vcfR package to the Dockerfile. This now should be up to date with all packages and versioning we need for the repo!