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vctrymao

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Latest activity by vctrymao
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    vctrymao commented,

    1. Community
    2. Somatic
    3. MergeBamAlignment produces unknown error

    Actually, I noticed the command that is actually running. I think the problematic area is like you said, `-PROGRAM_GROUP_COMMAND_LINE bwa mem -K 100000000 -p -v 3 -t 4 -Y \/n/data1/hms/dbmi/park/DA...

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    vctrymao commented,

    1. Community
    2. Somatic
    3. MergeBamAlignment produces unknown error

    I don't think so? The command as written was executed. I also have run this script before on other samples with no issue.  There isn't really a stack trace, this occurs before anything really runs:...

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    vctrymao created a post,

    MergeBamAlignment produces unknown error

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    1. Community
    2. Somatic

    I am using MergeBamAlignment:  ``` java -Dsamjdk.compression_level=5 -Xms3000m -Xmx3200m -jar /n/data1/hms/dbmi/park/alon/software/picard.jar \MergeBamAlignment \VALIDATION_STRINGENCY=SILENT \EXPEC...

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    vctrymao created a post,

    Funcotator table format

    1. Community
    2. Germline

    Is it possible to use Funcotator for germline calls but format the output in a table format instead of a VCF? I understand that MAF isn't yet available for germline Funcotator, but is there any oth...

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    vctrymao created a post,

    Getting HaplotypeCaller SNP support in tumor

    1. Community
    2. Germline

    I have a list of germline SNPs from HaplotypeCaller. I want to get the read level information, etc. of these SNPs in the tumor BAM file and format it into a VCF (ie. to see the read level support f...

    • vctrymao
    • 2 followers
    • 2 comments
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    vctrymao commented,

    1. Community
    2. Germline
    3. HaplotypeCaller and low-VAF variants

    No, I'm just wondering how this might happen realistically. 

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    vctrymao created a post,

    HaplotypeCaller and low-VAF variants

    1. Community
    2. Germline

    I am using HaplotypeCaller to generate germline variants. I noticed that HaplotypeCaller calls some variants with very low VAF values (see below):  What is the reasoning behind this? In what situa...

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    • 3 comments
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    vctrymao commented,

    1. Community
    2. Somatic
    3. Missing mutations

    Could you explain how exactly GATK defines active regions? It isn't intuitive to me that Mutect2 would omit a region with high read level support.

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    vctrymao commented,

    1. Community
    2. Somatic
    3. Missing mutations

    I read this, but I did not see an exact description of what an "active region" is defined as mathematically. Regardless, this seems to have fixed the problem. 

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    vctrymao commented,

    1. Community
    2. Somatic
    3. Missing mutations

    I read that using `force-active` in Mutect2 may help. What exactly is this doing, and why is this turned off by default?