vittoria

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vittoria
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  • Dear friends, I generated a joint vcf file for a trio but I have problems visualizing it with igv. where can I find a sample file to see how a correct file should appear in igv? where is the information in each variant concerning the identity (son, …
  • sorry geraldine, I have the same problem a should produce a vcf file for a trio shall I use HaplotypeCaller with the dad. mum and son recal...bam files? how using three times -I dadrecal.bam -I mumrecal.bam -I kidrecal.bam -o triorawvariants? a…
  • Dear Sheila, thank you I understand that I have to run something like java -jar GenomeAnalysisToolkit.jar -R human_g1k_v37_decoy.fasta -T CalculateGenotypePosteriors --supporting 1000G_phase3_v4_20130502.sites.vcf -ped trio.ped -V recalibratedVari…
  • thank you sheila I understand that the first step is running java -jar GenomeAnalysisToolkit.jar -R human_g1k_v37_decoy.fasta -T CalculateGenotypePosteriors --supporting 1000G_phase3_v4_20130502.sites.vcf -ped trio.ped -V recalibratedVariants.vcf …
  • thank you vittoria
    in tabix Comment by vittoria June 2017
  • jDear all I have generated Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi with tabix when running RealignerTargetCreator should indicate the tbi file among the inputs? is it correct to us use -known Mills_and_1000G_gold_standard.indels.hg38.…