Column `BP1` can't be converted from character to logical

[sigven]

Column `BP1` can't be converted from character to logical

[sigven]

Hi @jxshi,
Thanks for using CPSR! I am in the process of releasing a major upgrade of cpsr. If you can share your VCF with me, I can demonstrate how the new report will look.

best,
Sigve

[jxshi]

Here is the link to the vcf file. The download link will be valid for 7 days. Thank you!

Cheers!

[sigven]

@jxshi, (cc @brucemoran)

I have uploaded an example report of your VCF from a CPSR run (v 0.4.0 - soon to be pushed to GitHub) here. Make sure you download the file to view the contents properly (Dropbox cannot show the HTML fully).

PS. CPSR/PCGR is not fond of multiallelic variants (unfortunately a common output by GATK). Ideally these records should be decomposed prior to your run

In summary, the new version of CPSR will

• make reports that are better structured according to the five-level classification scheme
• have a more comprehensive classification for variants not recorded in ClinVar (see Documentation part of the report)
• carry flexibility for the cancer predisposition geneset: users can choose from > 30 different "virtual gene panels" from Genomics England PanelApp in order to more flexibly interrogate a predisposition gene set of interest

thanks,
Sigve

[jxshi]

Hi Sigve, The new report look fantastic! Thank you for you help! Looking forward to the new release. Cheers! Jianxiang

…

________________________________ From: Sigve Nakken <[email protected]> Sent: Tuesday, May 7, 2019 12:30 PM To: sigven/cpsr Cc: Shi, Jianxiang; Mention Subject: Re: [sigven/cpsr] Column `BP1` can't be converted from character to logical (#10) @jxshi<https://github.com/jxshi>, (cc @brucemoran<https://github.com/brucemoran>) I have uploaded an example report of your VCF from a CPSR run (v 0.4.0 - soon to be pushed to GitHub) here<https://www.dropbox.com/s/se85erm4vs2tnyk/fam3010040.cpsr.grch37.html?dl=0>. Make sure you download the file to view the contents properly (Dropbox cannot show the HTML fully). PS. CPSR/PCGR is not fond of multiallelic variants (unfortunately a common output by GATK). Ideally these records should be decomposed prior to your run In summary, the new version of CPSR will * make reports that are better structured according to the five-level classification scheme * have a more comprehensive classification for variants not recorded in ClinVar (see Documentation part of the report) * carry flexibility for the cancer predisposition geneset: users can choose from > 30 different "virtual gene panels" from Genomics England PanelApp<https://panelapp.genomicsengland.co.uk/> in order to more flexibly interrogate a predisposition gene set of interest thanks, Sigve - You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub<#10 (comment)>, or mute the thread<https://github.com/notifications/unsubscribe-auth/AG4YXGGB37A7LT3LIULHYBDPUHDFHANCNFSM4HK6MX3Q>.