Qianru Lenus SUN
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Latest activity by Qianru Lenus SUN-
Qianru Lenus SUN commented,
Gökalp Çelik may I bother for your help? thanks! here is my contig.tsv
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Qianru Lenus SUN created a post,
DetermineGermlineContigPloidy generating error
REQUIRED for all errors and issues: a) GATK version used: b) Exact command used: c) Entire program log: gatk DetermineGermlineContigPloidy \--contig-ploidy-priors /path/contig_ploidy_priors_clean....
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Qianru Lenus SUN commented,
Gökalp Çelik Thank you so much! The issue got fixed! While, the error about R and ggplot2 and other dependencies version (I'm not sure) as shown as below, although with a .pdf generated, not sure...
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Qianru Lenus SUN commented,
Gökalp Çelik thanks! I have added the different types in one go (as previously I found in the VariantRecalibrator step, if i remove each annotation, e.g. QD, then the next error will be MQ, followi...
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Qianru Lenus SUN commented,
Gökalp Çelik Dear Celik, Thank you so much! I did check my sample.hc.vcf.gz (generated by gatk HaplotypeCaller), showing as below (i just screenshotted the first 3 pages), all the "##FILTER=<ID=xx...
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Qianru Lenus SUN commented,
Gökalp Çelik Genevieve Brandt (she/her) Dear developers, I have completed the VariantAnnotator successfully after running 23 hours, with generating the sample_VariantAnnotator.vcf. Next, the same e...
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Qianru Lenus SUN commented,
Gökalp Çelik Thanks! It worked after switching to the gatk BQSR recalibrated .bam. But may I know how long the gatk VariantAnnotator would run? seems there is no info online, and so far, it has las...
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Qianru Lenus SUN commented,
Gökalp Çelik Dear developer, may I have your idea on it? Thanks!
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Qianru Lenus SUN commented,
Hi dear developer, may I have your advice? Thanks so much!
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Qianru Lenus SUN commented,
Following the error above, I run the below (as firstly with error, showing samtools index, then I used the indexed .bam.bai): gatk VariantAnnotator \ -R /path/Homo_sapiens_assembly38.fasta \ -I /...