@Anna
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Activity overview
Latest activity by @Anna-
@Anna commented,
Hi Pamela, OK, I understand it. Again, thanks a lot for explaining this. It is truly helpful for me. Best regards
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@Anna commented,
Hi Pamela, Thank you so much for your explanatory answer. I have below two variants as an example of my doubt, hope that’s ok (I just copied 3 representative samples, as I have >200, all with DP...
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@Anna created a post,
VQSR vs Hard Filtering
Hi, I’m analyzing >200 human exomes following GATK Best Practices. I’ve tried to read all the GATK documentation about this, but I’d like to ask you something just to be sure. I understand that it ...
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@Anna commented,
Hi Pamela, I'm already checking the steps on those links. I was hoping for some tips on how to adjust that same pipeline to cfdna analysis. Even so, your suggestions are much appreciated. Let's see...
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@Anna created a post,
cfDNA targeted sequencing - analysis pipeline
Hi there, I have human DNA samples isolated from tissue and from plasma, which were targeted sequenced on Ion Torrent. I've read some papers and blogs about the data analysis pipeline, but it looks...
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@Anna commented,
Hi Genevieve, Yes, the problem was indeed with the tabix file. I ran it again after re-indexing and it gave me no errors. Thank you, Anna
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@Anna commented,
I notice that maybe it could be due to errors in the tabix file. I am re-tabixing the files and re-running GenomicsDBImport.I'll let you know if this was indeed the solution.
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@Anna commented,
A USER ERROR has occurred: Couldn't read file. Error was: Failure while waiting for FeatureReader to initialize with exception: java.lang.NumberFormatException: For input string: "GT:DP:GQ:MIN_DP:P...
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@Anna commented,
Hi Genevieve, With: gatk ValidateVariants -V A811.g.vcf --dbsnp dbsnp_138.hg19.vcf LOG: 18:53:39.469 INFO ValidateVariants - Java runtime: Java HotSpot(TM) 64-Bit Server VM v1.8.0_181-b1318:53:39.4...
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@Anna created a post,
genomicDBimport ERROR: java.lang.NumberFormatException: For input string
AnsweredHi there, I had to redo the calling of two of my samples, and now I am trying to redo my genomic database in order to replace these two samples. My script:module load gatk/4.0.10.0 gatk --java-opti...