FranBC
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Activity overview
Latest activity by FranBC-
FranBC commented,
Genevieve Brandt (she/her) No worries, thank you for flagging it as a potential bug! Regarding the VCF errors - thank you for running ValidateVariants and highlighting them to me, much appreciated!...
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FranBC commented,
Genevieve Brandt (she/her) Isn't it this line in the dict file: franbc@MacBook-Pro bwa-gatk % grep "HLA" Homo_sapiens_assembly38.dict @SQ SN:HLA-A*01:01:01:01 LN:3503 M5:01cd0df602495b044b2c214d69a...
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FranBC commented,
Genevieve Brandt (she/her) The file I used is: Homo_sapiens_assembly38.fasta
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FranBC commented,
Hi Genevieve, Thank you for the prompt reply. Apologies, I thought I had supplied this information - I am actually using the build hg38 + decoys fasta reference file (Homo_sapiens_assembly38.fasta)...
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FranBC commented,
Hi Pamela, The VCF contig headers do seem to match, so I've uploaded the files to the GATK FTP server as: CollectVariantCallingMetrics_dbsnp155_FranBC2.tar.gz Thanks and best regards, Francesca
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FranBC commented,
Dear GATK Team, I am having a similar issue to Yenan, when using CollectVariantCallingMetrics, was a cause/workaround ever found for this? I have no problem when using this tool with the GRCh38 dbS...