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Priyadarshini Thirunavukkarasu

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Latest activity by Priyadarshini Thirunavukkarasu
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    Priyadarshini Thirunavukkarasu created a post,

    Error exporting GVCF

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    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...

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    Priyadarshini Thirunavukkarasu commented,

    I want intervals list for GRCh38. The below excel file was from this link (for GRCh38) but it also shows intervals from Hg19: https://console.cloud.google.com/storage/browser/_details/gcp-public-da...

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    Priyadarshini Thirunavukkarasu commented,

    Hello Can I use the interval list from this link https://console.cloud.google.com/storage/browser/_details/gcp-public-data--broad-references/hg38/v0/HybSelOligos/whole_exome_illumina_coding_v1/whol...

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    Priyadarshini Thirunavukkarasu created a post,

    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...

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    Priyadarshini Thirunavukkarasu created a post,

    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...

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    Priyadarshini Thirunavukkarasu created a post,

    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...

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    Priyadarshini Thirunavukkarasu commented,

    09:05:18.765 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/scicore/soft/apps/GATK/4.0.8.1-foss-2018b-Python-3.6.6/gatk-package-4.0.8.1-local.jar!/com/intel/gkl/native/libg...

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    Priyadarshini Thirunavukkarasu commented,

    This is the command used: gatk CNNScoreVariants \-I /variants/1.bamout.bam \-V /variants/1.vcf.gz \-R /data/reference/gch38.fa \-O /variants/filtered/1_scored.vcf \--tensor-type read_tensor \--tran...

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    Priyadarshini Thirunavukkarasu commented,

    Hello I am using 2D model. I have given time limit as 6 days, so the process terminated after 6 days Total SNPs: 412511 Total Indels: 11413 Priya

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    Priyadarshini Thirunavukkarasu created a post,

    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...