Priyadarshini Thirunavukkarasu
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Latest activity by Priyadarshini Thirunavukkarasu-
Priyadarshini Thirunavukkarasu created a post,
Confirming variants
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...
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Priyadarshini Thirunavukkarasu commented,
When you do joint genotyping, it is at a given site the variant calling is done. So,the genotypes will different between these samples for the same snp at a given position
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Priyadarshini Thirunavukkarasu commented,
Did you check the genotype. If it is homozygous for the variant allele at a given position? I have run a different pipeline for my samples and it shows the similar variant allele at a given positio...
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Priyadarshini Thirunavukkarasu commented,
Thank you. Does these samples, have same type of variant at a given position. For example, if it is a missense mutation across all the samples at a given position or the type of mutation differs?.
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Priyadarshini Thirunavukkarasu commented,
Could you give an example?
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Priyadarshini Thirunavukkarasu commented,
But, do you see different variant type between the samples.
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Priyadarshini Thirunavukkarasu commented,
I compared to the dataset (HG001_GRCh38_1_22_v4.2.1_benchmark.vcf.gz) from Genome in bottle database Is there way to check the pipeline which you are following to call and filter variants with an...
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Priyadarshini Thirunavukkarasu created a post,
False negatives in variant evaluation step
AnsweredI 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...
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Priyadarshini Thirunavukkarasu created a post,
Error exporting GVCF
AnsweredHello 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...