Monete

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Monete
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Brazil
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  • 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). …
  • 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…