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Priyadarshini Thirunavukkarasu

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Recent activity by Priyadarshini Thirunavukkarasu Sort by recent activity Recent activity 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

  • Errors in bam files

    Answered
    1. Community
    2. Germline

    Hello I am stuck in one of the preprocessing steps for exome analysis. Created unmapped and sorted bam files from original fastq files. Also, created aligned and sorted bam files. The unmapped and ...

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