Heads up:
We’re moving the GATK website, docs and forum to a new platform. Read the full story and breakdown of key changes on this blog.

aaronchu

About

Username
aaronchu
Location
US
Joined
Visits
134
Last Active
Roles
Member
Points
24
Badges
5
Location
US

Comments

  • Thanks Sheila! The referred question does have relevance here. It seems the current gatk will not calculate confidence for invariant sites, so I can currently get only confident 0/0 for sites that show at least one variant allele call in the populat…
  • I attached six gvcf files for which I ran GenotypeGVCFs with -inv to jointly genotype all confident sites. GenotypeGVCFs command: java -jar /programs/GenomeAnalysisTK-3.1-1/GenomeAnalysisTK.jar -nt 4 -R hs37d5.fa -T GenotypeGVCFs -inv \ -V /gvcf/SQ…
  • I think I can avoid this problem. The problematic trio vcf file was extracted by SelectVariants from a master vcf file jointly called for many samples. Now I just run PhaseByTransmission with --pedigreeValidationType SILENT on the master vcf file (w…
  • Hi Geraldine, sorry I just saw your response. Usually I got an email for a response to my question, but this time I didn't. I try to make a snippet for the vcf file (covering the problematic site which stops the job) but when I run the snippet it ca…
  • By the way, the input vcf is generated by GenotypeGVCFs (3.1.1). When I sued PhaseByTransmission in 2.8.1 to phase a jointly called trio vcf, it worked without any problem. (Quote)
  • Hi there, I met exactly the same problem with PhaseByTransmission in 3.1.1. It generated a truncated vcf containing the first few lines of phased vcf and then stopped wth the same error reported. Could you take a look at this? Thanks! aaron (Quote)
  • Thanks Eric! I attached the test bam files here. There are 3 bams within the NA12878 trio each containing alignments within +/- 300 bp regions centered at each of the 49 validated de novo SNV site. The list of 49 sites is also attached. The 7 sites …