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2 hours ago by

It seems like my VCF's header contains at least an empty smaple ID. I am not sure how to figure out where it goes wrong because, if I run awk 'print NF', all lines have the same number of fields.

When I ran bcftools, it told me
"[E::bcf_hdr_add_sample] Empty sample name: trailing spaces/tabs in the header line?"

And when I ran refinedIBD, it gives an error of the same reason

java -jar ../../../../tools/refined-ibd.17Jan20.102.jar gt=test.vcf out=test ERROR: java.lang.IllegalArgumentException: id.isEmpty()
java.lang.IllegalArgumentException: id.isEmpty()
at beagleutil.SampleIds.getIndices(
at beagleutil.Samples.fromIds(
at vcf.VcfHeader.samples(
at vcf.VcfHeader.<init>(
at vcf.RefIt.<init>(
at vcf.RefIt.create(
at refined.RefinedIbd.lambda$windowIt$0(
at vcf.WindowIt$
at terminating program.

Yet I couldn't locate which column in the #header line goes wrong. Can anyone help? Thanks a lot!


2 hours ago


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