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Kshama Aswath

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Latest activity by Kshama Aswath
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    Kshama Aswath commented,

    1. Community
    2. Germline
    3. VQSR positive training model failed to converge

    Hi , I was getting the same error on Indel recalibration and had to end up using max-gaussian to 1 ! Everything ran fine but I am nervous and uncertain on using that low number. What is the disadva...

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    Kshama Aswath commented,

    1. Technical Documentation
    2. Glossary
    3. GenomicsDB

    Hi all, I made GenomicsDB sometime ago with specific intervals (using bed files for the regions I need from Agilent exome padded regions of interest) and now we decided to explore another region th...

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    Kshama Aswath commented,

    1. Tool Index
    2. 4.1.4.1
    3. CalculateGenotypePosteriors

    Hi , I get this error when I use supporting population. If I run without it then it works. IS this coz my vcf input is a multisample input or is it some other reason?  Using GATK jar /usr/local/app...

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    Kshama Aswath commented,

    1. Community
    2. Germline
    3. Heterozygosity in VQSLOD

    Thankyou David ! I will give it a try and appreciate your time !

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    • Kshama Aswath
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    Kshama Aswath commented,

    1. Community
    2. Germline
    3. Heterozygosity in VQSLOD

    Thanks David, I appreciate your response! I had read that document a while ago and my questions are based on that document as it does not clearly say what to do in cases on having large samples but...

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    • Kshama Aswath
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    Kshama Aswath commented,

    1. Community
    2. Germline
    3. Heterozygosity in VQSLOD

    Hi, This is great! I had a few question regards to ExcessHet.  It mentions in the document to use excessHet across large number of unrelated samples. I have a cohort that includes many families, ca...

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    Kshama Aswath commented,

    1. Community
    2. Germline
    3. Cant find information from VQSR documentation links

    Thankyou Genevieve ! I found a VQSR video on youtube from you guys. I have seen the ones you have linked here but I cant find the exact document that the hyperlink in the document I have posted, le...

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    Kshama Aswath commented,

    1. Community
    2. Documentation Questions
    3. What is the correct step? VQSR and CNNScoreVariants?

    Hi Damian, I am a pretty new user of GATK pipeline myself and am drowned in reading documentation after documentation and many times end up finding out "new steps" to use accidentally on GATK searc...

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    Kshama Aswath created a post,

    Cant find information from VQSR documentation links

    1. Community
    2. Germline

    Hi all, Although I love GATK pipeline for all the support and documentation, it is kind of hard to find the recently updated documentations for many of the steps given in GATK. My experience has be...

    • Kshama Aswath
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    • 8 comments
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    Kshama Aswath commented,

    1. Community
    2. Germline
    3. Why am I getting an error in genotypeGVCF on newQual?

    Hi Genevieve, I cant find that post now ! Maybe it is updated already?  Sometimes it gets so treacherous skimming through all these various posts updated at different dates etc.  I always go with t...