mmaj

About

Username
mmaj
Joined
Visits
114
Last Active
Roles
Member
Points
42
Badges
8
Full Name
Mads Malik Aagaard Jørgensen

Comments

  • Hi Geraldine, Thanks for the suggestion! I've rerun the HC command without downsampling (simply removing "-dt NONE" from above command), and it emits a DP around 200 reads, which (albeit being only 1/3 of the total reads for this position)…
  • Hi sheila, I'm using GATK v3-2.2. command: -T HaplotypeCaller --dbsnp $dbSNP -I sample.bam -rf MappingQualityZero -pairHMM VECTOR_LOGLESS_CACHING -o sample.raw.HTC.vcf -R $fastaref -L $ROI -minPruning 2 -nct $threads -dt NONE From this run, we los…
  • Hi Sheila and Geraldine, While it may not seem like a bug, I must admit I have a hard time understanding how HC selects a tiny subset of (what appears to be) perfectly good reads in our amplicon sequencing setup. In a very recent sample, we have +60…
  • Hi Geraldine (and others). We're experiencing similar problems with the Haplotypecaller (both v3.1-1 and v3.2-2). In fact our problem is almost identical to that reported by Ryan, a few posts back in this thread. We use amplicon sequencing and conse…
  • Ok, thanks!