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Using snpsift to annotate vcf with dbsnp and Clinvar
written by whb 6snpsift website shows how to annotate variants with dbsnp (one file). java -jar SnpSift.jar annotate dbSnp132.vcf variants.vcf > variants_annotated.vcf but if I want annotate using …
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SnpSift to annotate vcf with multiple databases
written by whb 6Hi, Should I annotate the vcf file with multiple databases e.g. dbSNP, 1000genome, ClinVar and dbNSFP if the panel contains mostly coding and some intronic …
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Gene expression and chromatin state
written by whb 6I want to compare the expression of a list of genes (mouse) in a specific organ e.g. lung. Also, the chromatin state e.g. which regions …
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Filtering vcf with dbSNP
written by whb 6Hi, From NCBI website, dbSNP accepts both disease or not SNPs [https://www.ncbi.nlm.nih.gov/books/NBK44447/#Content.what_classes_of_genetic_variatio][1]. I have some samples that do not have matching normals. I have done …
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Different dbSNP files input yield different variants?
written by whb 6Hi I was trying to compare if using different dbSNP file as input of `BaseRecalibrator` and `Mutect2` gives different results. and it gave entire different …
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Known-variant and AF-only files of GATK Mutect2 on Mouse DNA sequencing data
written by whb 6I have some mouse C57 targeted panel sequencing data. I want to call somatic variants using GATK. Because of the cost, there are only 4 …
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Heterozygous individuals and FastaAlternateReferenceMarker
written by gubrins 35Good afternoon, I am having a doubt with the function `FastaAlternateReferenceMarker` from GATK. I already have a phased VCF file and when I want to …
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dbsnp in vcf format compatible with hg38
written by apocalyps52 4Hello, I need to annotate the snps in a vcf file that I generated from hg38 reference. I try to use SnpSift for annotation however …
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Ncbi Length Search
written by Nicolas Rosewick 1.1K<p>Hi,</p> <p>Is it possible to specify the nucleotide length limit in a ncbi search ? I don't find anything on the NCBI website about this …
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Dbsnp Individual Genotyping Information For Specific Snps
written by Andrea_Bio 286<p>Hello</p> <p>I've gone through the schema for dbSNP 132 quite thoroughly and it looks like it is not possible to find the genotype for individuals …