Priyadarshini Thirunavukkarasu
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Recent activity by Priyadarshini Thirunavukkarasu Sort by recent activity-
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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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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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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Could you give an example?
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But, do you see different variant type between the samples.
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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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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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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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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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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...