Can HaplotypeCaller be used on drug treated samples?

Hello, I am working on a RNASeq data which consists of liver samples from donors. It is a case-control study where 12 samples are divided as Normal (control) and Rifampin Treated (case). I want to create a sample specific VCF file. I was going through the documentation and I got a bit confused between HaplotypeCaller and Mutect2. Which one should I use to get my VCF file.

In addition, is there a decent way to add gene name, symbol and other annotations to the INFO field of the VCF file?

Any help is much appreciated.

Regards,
Anurag

Best Answer

Answers

  • Hi @EADG Thank you for the reply. Let me check it out.

  • SheilaSheila Broad InstituteMember, Broadie, Moderator

    @anuragpassi
    Hi Anurag,

    Can you clarify what your end goal is? Mutect2 is specifically designed for detecting somatic variants. If you are interested in comparing the germline variants in your case and control samples, it may be best to use HaplotypeCaller.

    -Sheila

  • Hello @Sheila As I mentioned the data is for Liver hepatocytes (somatic). So lets say the RNAseq data contains 6 untreated samples and 6 treated samples with Rifampin. So I do need to compare the case and control but these are somatic variants. Should i be using Mutect2 or HaplotyCaller.

    Regards,
    Anurag

  • SheilaSheila Broad InstituteMember, Broadie, Moderator

    @anuragpassi
    Hi Anurag,

    Thanks for the clarification. For somatic samples, you should indeed use Mutect2. I thought you were trying to compare germline variants.

    -Sheila

  • Hi @EADG @Sheila , I am revisiting this query that I had. I want to get some clarification regarding Mutect2 and HaplotypeCaller. People who have used Mutect2 have used it for Cancer data. However, my data is not a Cancer data. It is a RNAseq data for liver hepatocytes with some samples treated with rifampicin and others not. So, I have some questions:
    1) Mutect2 caters to cancer data better and/or is it specific for cancer data?
    2) If I am looking for variations in a non-cancer data, Mutect2 should work?

    Regards,
    Anurag

  • Hello @shlee, @Sheila In addition to the above query I wanted to add some queries. Actually, since I am working with RNASeq data where there are 12 liver tissue samples from 6 patients (case and control for each). The case samples are liver samples treated with rifampicin and control is without rifampicin. This is not a Cancer study. I want to identify SNPs in those samples. I have read the documentation for MuTect and HaplotypeCaller both. I am some questions:

    1) People have used Mutect2 only for cancer data. So, I cannot use it for my data?
    2) Is it necessary to create a PON file? If yes, will i be making the PON file with the Control samples of the 6 donors and merging them into one?
    3) What if I used HC to identify variants in my 12 sample files (both normal and treated samples). Will it be wrong?

    I am rather confused in this step. Kindly help.

    Regards,
    Anurag

  • shleeshlee CambridgeMember, Broadie, Moderator
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