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Priyadarshini Thirunavukkarasu

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Recent activity by Priyadarshini Thirunavukkarasu Sort by recent activity Recent activity Votes

  • Confirming variants

    1. Community
    2. Germline

    Hello, I performed whole exome analysis using GATK pipeline. After annotation of variant using annovar, I performed these steps: Filtered variants that have passed all filters Using Gnomad_exome_a...

    • Priyadarshini Thirunavukkarasu
    • 2 followers
    • 1 comment
    • 0 votes

  • False negatives in variant evaluation step

    Answered
    1. Community
    2. General Discussion

    I have whole exome data from 6 subjects. I followed the GATK pipeline for preprocessing, then joint genotyped and hard filtered the variants using the default thresholds. I did variant evaluation u...

    • Priyadarshini Thirunavukkarasu
    • Edited
    • 2 followers
    • 4 comments
    • 0 votes

  • Error exporting GVCF

    Answered
    1. Community
    2. General Discussion

    Hello Please find the code used for exporting GVCF to genomic database and the error as well. I tried renaming the interval list file but still get the error. Please advice Version: GATK/4.2.2.0-f...

    • Priyadarshini Thirunavukkarasu
    • Edited
    • 2 followers
    • 1 comment
    • 0 votes

  • Reference genome to create intervals list

    1. Community
    2. General Discussion

    Hello I have short read exome data. For creating intervals, I converted the reference fasta  file to reference bed file and used this bed file as list of intervals. I used this intervals list for s...

    • Priyadarshini Thirunavukkarasu
    • 2 followers
    • 5 comments
    • 0 votes

  • Intrerval list from bed file

    1. Community
    2. General Discussion

    Hello I am trying to convert my bed file as intervals list. My reference dictionary and bed file are from same genomic build GRCh38. But still it gives the below error   java -jar $EBROOTPICARD/pic...

    • Priyadarshini Thirunavukkarasu
    • 2 followers
    • 1 comment
    • 0 votes

  • Individual versus joint variant calling

    1. Community
    2. General Discussion

    Hello I need a suggestion. I have exome data of 6 subjects. As the sample size is very less, should we do variant calling on every sample rather than joint variant calling?. As joint variant callin...

    • Priyadarshini Thirunavukkarasu
    • Edited
    • 3 followers
    • 1 comment
    • 0 votes

  • Filter variants

    1. Community
    2. Germline

    Hello I am running convolutional neural networks to filter variants (https://gatk.broadinstitute.org/hc/en-us/articles/360037226672-CNNScoreVariants). Is this step computationally intensive step, i...

    • Priyadarshini Thirunavukkarasu
    • 2 followers
    • 7 comments
    • 0 votes

  • Running CNN Score Variants

    1. Community
    2. Germline

    Hello I am running GATK/4.2.2.0-foss-2018b-Java-1.8. When I try to run the CNNScoreVariants, I get the below error: python exited with 1Command Line: python -c import gatktoolStdout: Stderr: Traceb...

    • Priyadarshini Thirunavukkarasu
    • 2 followers
    • 1 comment
    • 0 votes

  • Funcotator data source

    1. Community
    2. Germline

    Hello I loaded the GATK 4.2.2.0 How to extract data sources using the below command: FuncotatorDataSourceDownloader --germline --validate-integrity --extract-after-download I get the following err...

    • Priyadarshini Thirunavukkarasu
    • Edited
    • 2 followers
    • 5 comments
    • 0 votes

  • Base recalibration

    1. Community
    2. Germline

    Hello I need suggestions in creating index and dictionary with vcf files. For the base recalibration step, I downloaded Homo_sapiens_assembly38.known_indels.vcf.gz from the given link: https://cons...

    • Priyadarshini Thirunavukkarasu
    • Edited
    • 2 followers
    • 7 comments
    • 0 votes