Priyadarshini Thirunavukkarasu

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Recent activity by Priyadarshini Thirunavukkarasu Sort by recent activity Recent activity Votes
  • False negatives in variant evaluation step


    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...

  • Error exporting GVCF


    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/

  • Reference genome to create intervals list

    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...

  • Intrerval list from bed file

    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...

  • Individual versus joint variant calling

    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...

  • Filter variants

    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...

  • Running CNN Score Variants

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

  • Funcotator data source

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

  • Base recalibration

    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...

  • Errors in bam files


    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 ...