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Replies: 1 comment · 4 replies
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@lecb Based on the current documentation we recommend you use the
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Amazing, it works! Thanks so much :-) |
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I spoke too soon - it failed. There seems to be an issue with weird chromosomes (see below). I'm loading in a single sample genome processed with GATK4. One other thing, previously we used 'don't validate' because the log file was too big for our VM. I can't see from the documentation where I can change this to be true.
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If you need to use the "don't validate" flag, you can copy the failing command that the bash script generates and add the don't validate flag and run the modfied command directly. Its a bit less user friendly than the script because it won't stay up to date, but it will work |
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Brilliant, thanks Hana! |
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This discussion was converted from issue #2982 on October 03, 2022 14:57.
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Hello,
I'm trying to load some WGS data into our local Southampton version of seqr and despite this working before, I'm getting the below error.
I'm definitely executing from the correct directory and the file
/input_vcfs/SOPR0402.vcf.gz
is in the correct location and exists.Any advice would be gratefully received.
Ellie
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