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PostsRecent activity by Priyadarshini Thirunavukkarasu Sort by recent activity
False negatives in variant evaluation stepAnswered
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 GVCFAnswered
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/188.8.131.52-f...
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...
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/184.108.40.206-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...
Funcotator data source
Hello I loaded the GATK 220.127.116.11 How to extract data sources using the below command: FuncotatorDataSourceDownloader --germline --validate-integrity --extract-after-download I get the following err...
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 filesAnswered
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 ...