
fabienne JABOT-HANIN
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Latest activity by fabienne JABOT-HANIN-
fabienne JABOT-HANIN commented,
Hi Genevieve, Thank you for your suggestions. I've tried with the --linked-de-bruijn-graph option and the variant doesn't appear anymore. This seems to fix the problem ! Great ! So, does its mean t...
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fabienne JABOT-HANIN commented,
Hi Genevieve, I've uploaded the files to your ftp server. The name of the file is : Fabienne_JABOT-HANIN_bug_report.zip I hope you will find what's happening there. Best Fabienne
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fabienne JABOT-HANIN commented,
Genevieve, I try GATK 4.2.0.0 and I have the same variant in the vcf after HaplotypeCaller : chr17 78064001 . G A 469.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.082;DP=384;ExcessHet=3.0103;FS=65.619;ML...
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fabienne JABOT-HANIN commented,
Hi Genevieve, Here you could find the bamout with the ArtificialHaplotypeRG : And the view of the original bam : I'm going to install and try the GATK4.2.0.0 and teel you if it's always the sam...
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fabienne JABOT-HANIN commented,
Here is attached the screenshot of the location in IGV in the bamout : The variant is called at : chr17 78064001 . G A 469.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.082;DP=368;ExcessHet=3.0103;FS=81....
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fabienne JABOT-HANIN commented,
Hi Genevieve, That's what I did, and in the bamout file, there were only 4 reads supporting the alternative allele, whereas in the gvcf and vcf AD mentioned 106 REF / 86 ALT. Do you want me to send...
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fabienne JABOT-HANIN created a post,
Haplotypecaller : variant calling not seen in bamout alignments
AnsweredGATK v4.1.3.0 c) Why do I see (......)? Hello, I'm using GATK v4.1.3.0 to call variants from short reads with Haplotypecaller. In the gvcf and vcf resulting from the command line, a variant is ca...