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SampleID input parameter #175

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aokulabasile opened this issue Apr 6, 2023 · 2 comments
Open

SampleID input parameter #175

aokulabasile opened this issue Apr 6, 2023 · 2 comments

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@aokulabasile
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Hi,

Would it be possible to add an input parameter for sample name specification? Currently, EH reads the sampleID from the bam file name auto sampleId = boostHtsFilePath.stem().string() , and this may not always be the accurate sampleID. The addition of a sampleID input parameter would be very helpful. Thanks!
@dennishendriksen
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workaround:

echo -e "MY_SAMPLE_ID" > samples.txt
bcftools reheader --samples samples.txt expansionhunter_output.vcf

@andreasssh
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Might be too late, but I added this option into my fork of EH: https://gitlab.com/andreassh/ExpansionHunter

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@dennishendriksen @aokulabasile @andreasssh