Avatar

LP

Follow
  • Total activity 14
  • Last activity
  • Member since
  • Following 0 users
  • Followed by 0 users
  • Votes 8
  • Subscriptions 1

Comments

Recent activity by LP Sort by recent activity Recent activity Votes
    1. Community
    2. Germline
    3. Variant filtered from GVCF

    Hi Genevieve, We repeated the analysis with GATK 4.2.1 with --linked-de-bruijn-graph enabled and the variant now survives to the VCF! We are not sure yet if this is because the new version or becau...

    1. Community
    2. Germline
    3. Variant filtered from GVCF

    Hi Genevieve, I ran this: gatk GenotypeGVCFs --output allsites.vcf --reference Homo_sapiens_assembly38.fasta --variant Sample_A.g.vcf.gz --include-non-variant-sites true --intervals chr20:4690000-4...

    1. Community
    2. Germline
    3. Variant filtered from GVCF

    Hi Genevieve, I have attached a screenshot from IGV for the HaplotypeCaller bam, with the variant highlighted (from Sample A). How do you force the variant to be called by GenotypeGVCFs? Many thank...

    1. Community
    2. Germline
    3. Variant filtered from GVCF

    Hi Genevieve, Thank you for your help! I have looked at the trouble shooting doc.  The expected variant was called at the site of interest in the GCVF (see above), but excluded from the VCF by Geno...