difference in query_only labels in basic vs annotate_multisample?

[haffenerpaige]

Hello!

I have been running needLR_basic on per-sample SV VCFs as well as needLR_annotate_multisample on a merged VCF of the same samples. In the per-sample VCFs there is a SV being identified as "query_only" in a couple of the samples which I understand as being absent from the 1000G cohort. However, that same SV is present in the merged VCF of the same samples and needlr_annotate_multisample does not identify it as "query_only". Is there a difference in the "query_only" labels added to SVs in needLR_basic and needler_annotate_multisample?

Thanks for your help!
Paige

[jgust1]

Hi Paige, Yes - needLR_annotate_multisample does not merge the samples from your query vcf with the samples from the 1000G cohort/ does not calculate relative allele frequencies, it simply annotates the SVs in your vcf with the annotations that are part of needLR (genomic context, disease-association, etc). Best, Gus

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On Mon, Jun 23, 2025 at 7:52 AM haffenerpaige ***@***.***> wrote: *haffenerpaige* created an issue (jgust1/needLR#7) <https://urldefense.com/v3/__https://github.com/jgust1/needLR/issues/7__;!!K-Hz7m0Vt54!g_4oAHSi1gxMwagf1p1WVFF0BrQHYXkp175a2ezRmOaoxP2oattF3DkSCrYByLtqwh3cmJJ5SXh-li7VS7FWzJE$> Hello! I have been running needLR_basic on per-sample SV VCFs as well as needLR_annotate_multisample on a merged VCF of the same samples. In the per-sample VCFs there is a SV being identified as "query_only" in a couple of the samples which I understand as being absent from the 1000G cohort. However, that same SV is present in the merged VCF of the same samples and needlr_annotate_multisample does not identify it as "query_only". Is there a difference in the "query_only" labels added to SVs in needLR_basic and needler_annotate_multisample? Thanks for your help! Paige — Reply to this email directly, view it on GitHub <https://urldefense.com/v3/__https://github.com/jgust1/needLR/issues/7__;!!K-Hz7m0Vt54!g_4oAHSi1gxMwagf1p1WVFF0BrQHYXkp175a2ezRmOaoxP2oattF3DkSCrYByLtqwh3cmJJ5SXh-li7VS7FWzJE$>, or unsubscribe <https://urldefense.com/v3/__https://github.com/notifications/unsubscribe-auth/A3LED75Z3ZRCLDS3YYKECDL3FAIBDAVCNFSM6AAAAAB75UOMG2VHI2DSMVQWIX3LMV43ASLTON2WKOZTGE3DQNBZGI2TQNY__;!!K-Hz7m0Vt54!g_4oAHSi1gxMwagf1p1WVFF0BrQHYXkp175a2ezRmOaoxP2oattF3DkSCrYByLtqwh3cmJJ5SXh-li7VO6ixGQM$> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>