@Anna
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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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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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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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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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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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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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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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Ok, I will try that. Thank you so much for your help!
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I used gatk/4.0.10.0 on all the steps until the genotyping. The genotyping went well for chr 1-15, but for the rest it was taking too long (event when I tried using smaller intervals). So I have tr...
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Hi Genevieve, I'm sorry. All vcf files were created with gatk/4.0.10.0. I could eventually do the calling with the updated version, but only for some of the samples. The batch is the same for chr...