short tandem duplication

[MartaRusmini]

Hi
I run VALOR2 to my data from linked-read sequencing. I have a sample with a known tandem duplication of 13Kbps and, although I can see the duplication in the bam (for example through IGV) it cannot be called by the tool. I read from the paper that the tool is able to call larger segmental duplication (>40Kbps). Is it right? Is it a way or configuration to call smaller variations? Thank you

[f0t1h]

Hi @MartaRusmini,

VALOR2 algorithm focuses on the larger variants. The minimum size of the called variants is strictly limited by the molecule size of the linked reads. For shorter variants (< (1 molecule size) Bps), I suggest using Longranger or some other linked read SV discovery tool.

Thank you for your interest.

[MartaRusmini]

thank you for your reply may I also ask if you could help me to understand the output? In particular, I would like to understand what "pm", "mp", "mm", "pp" and their combination mean. I didn't find anything about that in the guide but, maybe, I wrong something Il giorno gio 13 gen 2022 alle ore 16:16 Fatih Karaoglanoglu < ***@***.***> ha scritto:

…

Hi @MartaRusmini <https://github.com/MartaRusmini>, VALOR2 algorithm focuses on the larger variants. The minimum size of the called variants is strictly limited by the molecule size of the linked reads. For shorter variants (< (1 molecule size) Bps), I suggest using Longranger or some other linked read SV discovery tool. Thank you for your interest. — Reply to this email directly, view it on GitHub <#13 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AN4EQYJT5NYFCQR2TP5ONC3UV3UGVANCNFSM5L3LWGDQ> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>. You are receiving this because you were mentioned.Message ID: ***@***.***>

-- *Rusmini Marta, PhD* UOSD Genetica e Genomica delle malattie rare Servizio di Bioinformatica Clinica Istituto Giannina Gaslini via Gaslini, 5, 16148 Genova-Quarto, Italy tel. (0039)010-56363932 Computational and Chemical Biology Istituto Italiano di Tecnologia IIT ***@***.*** ***@***.***>* Via Enrico Melen, 83 Edificio B Piano 8, 16152 Genova P Please consider the environment before printing this email. Think green

[f0t1h]

(p)lus and (m)inus shows the short paired read mapping orientation. Each, pm, mp, mm and pp shows the number of supporting discordant reads for the SV with the said orientation. Each SV type creates 2 (or 3 for translocation) different short read support. Please look at the Figure 1 in the VALOR2 paper for the details.