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  • Hi Any info (or news) about workshop on August 26-29 at São Paulo, Brazil? Thank you very much
  • Thanks @bhanuGandham for your prompt reply And another question about SAC annotation: the reads counted in such annotation are informative reads (as same as in DP annotation) or are unfiltered count of reads (as same as in AD annotation)?
  • Hi, I don't know if @pjongeneel solved this problem. But I also have the same question every time that I had to choose some annotation. Since I couldn't find a complete answer, I put here my solution (sounds archaic, maybe there is something bette…
  • Hi @AdelaideR Here it is a screenshot from my comment box (below). I use markdown codes (independently from this menu) and doesn't work also. I'm using google chrome also (Version 73.0.3683.75). Could be problems of my browser?
  • Thanks @SChaluvadi I think I'll proceed with "selectvariants" in order to remove such false positives out before genotype refinement. Thanks for your great explanation.
  • Hi @SpaceCade7 Since I started my posts here I was able to use markdown formatting. I don't know why, suddenly, markdown stopped work for me. Is there anything which I can do? Sorry If I'm asking this in wrong place. Thanks
  • Hi @SChaluvadi Thanks for your reply. The snippets from my vcf, presented above, came out from vqsr steps (VariantRecalibrator and Applyrecalibration). So I already did this. That's why my vcf is tagged with PASS or VQSR tranches each variant…
  • Hi @SChaluvadi (sorry, my markdown doesn't work for a long time, and I don't know why and who to ask for help) Considering this description about vqsr steps (from: https : / / software . broadinstitute . org / gatk / documentation / article ? id…
  • Thanks for your prompt answer @SChaluvadi Just to check: I have a vcf with ~6.500.000 variants and ~5.900.000 of those have "PASS" in their INFO field. So, like you said, genotype refinement steps will only work with such ~5.900.000 v…
  • Hi @bhanuGandham thanks for your reply Now I unterstood. I thought "lowGQ/PASS" tags were from "GQ" information updated. Thank you very much for your help and patience.
  • Hi @bhanuGandham Thank you so much for your help. Now I'm trying picard liftovervcf from b37 to hg19. Besides the topic of this discussion, It was hard to find the chain file. But now, I got it! :-D Mainly, because the ftp address you sent,…
  • Hi @bhanuGandham Thanks for your reply. For now, we will continue on 3.8 version in order to try to replicate some results. Also, I believe it's important to say this error didn't happen with commands below (despite the same input datasets). java…
  • Hi @bhanuGandham My command (with ERROR described above) was: java -Xmx480000m -jar $gatkPath -R hg19.fasta -T GenotypeGVCFs -nt 20 \--dbsnp dbsnp_138.hg19.vcf --variant ${fileName}-cohort_COMBINED.g.vcf.gz \--annotateNDA --sample_ploidy 182 --use…