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Slice .vcf files from TCGA controlled access during download

I'm interested in downloading TCGA controlled access data and have the permissions to do so. I have a list of file IDs for .vcf files for download, but would like to slice them before download because I do not need annotations from the entire genome. Does anyone know how to do this?

For reference, I was able to do this for controlled access bam files with the following command after exporting the authorization token: 

for id in $(cat file_ids.txt)
do
    curl --header "X-Auth-Token:$token" "https://api.gdc.cancer.gov/slicing/view/${id}?gencode=my_gene" \
        --output desitination/${id}.bam
done
vcf tcga bcftools vcftools tabix
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updated by Ram Ram • written by j.lunger18 • j.lunger18

Please use the formatting bar (especially the code option) to present your post better. You can use backticks for inline code (`text` becomes text), or select a chunk of text and use the highlighted button to format it as a code block. I've done it for you this time.
code_formatting

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written by Ram Ram

Hello j.lunger18!

Questions similar to yours can already be found at:

We have closed your question to allow us to keep similar content in the same thread.

If you disagree with this please tell us why in a reply below. We'll be happy to talk about it.

Cheers!

PS: Please do not open multiple posts on the same problem. It would be better if you edit the other question and include the content from this one into it so we have information focused in one threads rather then split over multiple ones.

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written by ATpoint ATpoint

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