rename sample in GVCF file

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Bekah W

• November 23, 2021 22:08

Hiya,
I have been trying to rename sample in single sample GVCF using the picard  RenameSampleInVcf function. However it gives me ERROR: Invalid argument '50'.

Input: picard RenameSampleInVcf \
I=Pathtoinput.g.vcf \
O=/Pathtooutput.g.vcf \
OLD_SAMPLE_NAME=sample 50 \
NEW_SAMPLE_NAME=sample 1050;

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  Genevieve Brandt (she/her)

  • November 24, 2021 17:33

  Hi Bekah W,

  I think the issue is coming from the space in your sample name 'sample 50'. You could try specifying the sample name with single quotes so that the program reads the name correctly. For best practices, I would not recommend having a space in your sample name, it can cause many issues when manipulating your files.

  Best,

  Genevieve

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  Bekah W

  • November 24, 2021 20:48

  Cheers I realised it was actually just labelled 50 and not sample 50, it still didnt like this, so just removed the old name option entirely and it ran fine! Thank you, Best wishes, Bekah

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  Genevieve Brandt (she/her)

  • November 30, 2021 20:13

  Good news! Thanks for the update!

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