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ICGC Variant Calling Pipelines

Hi,

I would like to ask if any of you know the callers of the pipelines that are stated on ICGC such as broad, embl and sanger? I checked the metadata however the website which directed me required id/password accession. These are pipelines that were used for calling mutations which produced VCF files.

Thank you

Best,
Tunc

mutation-calling icgc
• 4,738 views • link
updated by Ram Ram • written by morovatunc morovatunc

1 answer

Can you put the link you have been looking into? Usually the broad mutation caller is GATK toolkit and Mutect. Often VarScan2 is also used widely. But am assuming that this one you are looking into are the ICGC -TCGA project which is run by multiple sites in the world. I not sure if the publication is out yet. So it shows only the status of the calls made at all different contributing sites that are a part of this challenge so sequence WGS for large PAN-Cancer panel.

You can take a look at this link which has a somatic workflow for SNVs . This is of Sanger

I am not sure for the embl but Delly is one which is widely used but that is for SVs and not SNVs. I guess you have to do a bit more digging.

As I said you can find the below links for the different workflows that are being used by 3 major workflow managers , and I believe this is being circulated across different centers where samples are being analyzed.

I think this link has most of the necessary information you are looking for.

• 0 views • link
updated by Ram Ram • written by ivivek_ngs ivivek_ngs

I am trying to get information about all the prostate cancer patients mutation calls. Therefore, I don't aim a specific file. Filter of the VCF have 3 options which you also stated; EMBL/DKFZ, Broad and Sanger. Thank you very much tho.

Also one more question, this kind of irrelevant to this topic but, When I download VCF which belongs to Sanger workflow. I couldn't open them with text edit. Shouldn't vcf be in text file format?

Thank you very much for your contribution. I almost got my hope about this fact.

Tunc

• 0 views • link
updated by Ram Ram • written by morovatunc morovatunc

First of all I would be a bit greedy , if you find my answer helpful please accept it as answer and upvote the same and also if any comments and reply are helpful then you can upvote them so that anyone else having similar questions can refer to it as well.

Coming to your second question you can always use some packages dedicated to VCF in R or bedtools to see the VCF format file. I am supposing the files you download are compressed so you cannot see them in text edit. You can download them and open in terminal with nano or vim or if you want to do it locally you can open them in excel. Or you can just awk the vcf files to get the columns you are interested in for your downstream use.

VCFTools

BEDTools

I believe this would suffice.

• 0 views • link
updated by Ram Ram • written by ivivek_ngs ivivek_ngs

I am trying to get information about all the prostate cancer patients mutation calls. Therefore, I dont aim a specific file. Filter of the VCF have 3 options which you also stated; EMBL/DKFZ, Broad and Sanger. Thank you very much tho.

Also one more question, this kind of irrelevant to this topic but, When I download VCF which belongs to Sanger workflow. I couldn't open them with text edit. Shouldn't vcf be in text file format?

Thank you very much for your contribution. I almost got my hope about this fact.

Tunc

• 0 views • link
updated by Ram Ram • written by morovatunc morovatunc

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