List of variants for Ingenuity Verification

[rachaelmein]

I have generated a list of variants that I would like to load into Ingenuity. I would like to use this list of variants to verify new updates of Ingenuity (similar to how the WES team do it). Are you able to convert this list into a format that can be uploaded to Ingenuity? The list of variants is saved here; P:\DNA LAB\Current\NGS worksheets\Ingenuity Panel Lists\Ingenuitys verification variants

Many thanks Rachael

[aledj2]

Hi Rachael, We're missing information from some of the variants to create these files. Would it be possible to provide for each variant the sample name (eg NGS215B_36_153071_VK_F_CMCMD_Pan1464) Thanks Aled

[rachaelmein]

Hi Aled

What information do you need? The problem is for the ones that a single sample is not listed (ie the ones that end in predicted deleterious) I got the variants from a batch analysis and therefore it will take me ages to go back to them to find out which sample it is on. I don’t want all variants for these samples I just want the variants I listed. I only put the analysis ID in the table for my records I didn’t think you would need this. What information does ingenuity need for it to be imported? I thought this could be done with non real data (ie. not from a VCF of seq data which include all variants).

I’m working from home today but it may be easier to discuss this face to face tomorrow to make sure we both understand what is needed and required here.

Thanks very much

Rachael

From: Aled Jones [mailto:notifications@github.com] Sent: 13 November 2018 10:32 To: moka-guys/helpdesk helpdesk@noreply.github.com Cc: Mein Rachael Rachael.Mein@viapath.co.uk; Author author@noreply.github.com Subject: Re: [moka-guys/helpdesk] List of variants for Ingenuity Verification (#342)

Hi Rachael, We're missing information from some of the variants to create these files. Would it be possible to provide for each variant the sample name (eg NGS215B_36_153071_VK_F_CMCMD_Pan1464) Thanks Aled

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttp://scanmail.trustwave.com/?c=8248&d=kajq2_XCVImQYrUhQzVbWDWOTCbvwGNPl-viryJ4sg&u=https%3a%2f%2fgithub%2ecom%2fmoka-guys%2fhelpdesk%2fissues%2f342%23issuecomment-438216533, or mute the threadhttp://scanmail.trustwave.com/?c=8248&d=kajq2_XCVImQYrUhQzVbWDWOTCbvwGNPl76-qnYstw&u=https%3a%2f%2fgithub%2ecom%2fnotifications%2funsubscribe-auth%2fAdw-GwSiDg50O0PzQ7P5dVtWYbK1v74zks5uup-VgaJpZM4YQcdi.

---

The information contained in this message and or attachments is intended only for the person or entity to which it is addressed and may contain confidential and/or privileged material. Unless otherwise specified, the opinions expressed herein do not necessarily represent those of Guy's and St Thomas' NHS Foundation Trust or any of its subsidiaries. The information contained in this e-mail may be subject to public disclosure under the Freedom of Information Act 2000. Unless the information is legally exempt from disclosure, the confidentiality of this e-mail and any replies cannot be guaranteed.

Any review, retransmission,dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipient is prohibited. If you received this in error, please contact the sender and delete the material from any system and destroy any copies.

We make every effort to keep our network free from viruses. However, it is your responsibility to ensure that this e-mail and any attachments are free of viruses as we can take no responsibility for any computer virus which might be transferred by way of this e-mail.

---

[aledj2]

Ingenuity requires a VCF and to create this VCF we need the REF and ALT which is different to the HGVS provided in the spreadsheet. We'd also need to provide all the fields that Ingenuity uses to filter (eg QC).

Therefore, we thought the easiest approach would be to download all the VCF files from the samples and write a script to pull out the specified variants from each file.

We may be able to find the VCF files with slightly less information than the full sample name, could you provide any of the following? DNA number Initials NGS run (eg NGS219A)

[rachaelmein]

To get DNA number and initials of specific samples I would have to go back into all of the runs. I could give you that information for the entire batch regardless of whether they have variant of interest or not. Then if you create a script to pull out specific variants it would just ignore those samples. Would that help?

Sorry this is proving more difficult than I envisaged. Sue had said some time ago that you could manually input a variant into ingenuity without any associated data so I thought this would be similar to how she did that.

Thanks Rachael

From: Aled Jones [mailto:notifications@github.com] Sent: 13 November 2018 10:57 To: moka-guys/helpdesk helpdesk@noreply.github.com Cc: Mein Rachael Rachael.Mein@viapath.co.uk; Author author@noreply.github.com Subject: Re: [moka-guys/helpdesk] List of variants for Ingenuity Verification (#342)

Ingenuity requires a VCF and to create this VCF we need the REF and ALT which is different to the HGVS provided in the spreadsheet. We'd also need to provide all the fields that Ingenuity uses to filter (eg QC).

Therefore, we thought the easiest approach would be to download all the VCF files from the samples and write a script to pull out the specified variants from each file.

We may be able to find the VCF files with slightly less information than the full sample name, could you provide any of the following? DNA number Initials NGS run (eg NGS219A)

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttp://scanmail.trustwave.com/?c=8248&d=lq7q2xOVRzbioiV_ncXLmMbeOmEiwee4zvJ9NWwXHg&u=https%3a%2f%2fgithub%2ecom%2fmoka-guys%2fhelpdesk%2fissues%2f342%23issuecomment-438224309, or mute the threadhttp://scanmail.trustwave.com/?c=8248&d=lq7q2xOVRzbioiV_ncXLmMbeOmEiwee4zqh_P2pFQw&u=https%3a%2f%2fgithub%2ecom%2fnotifications%2funsubscribe-auth%2fAdw-G8ZqKNjj08YKIv89pqrW6xUki3D8ks5uuqWYgaJpZM4YQcdi.

---

The information contained in this message and or attachments is intended only for the person or entity to which it is addressed and may contain confidential and/or privileged material. Unless otherwise specified, the opinions expressed herein do not necessarily represent those of Guy's and St Thomas' NHS Foundation Trust or any of its subsidiaries. The information contained in this e-mail may be subject to public disclosure under the Freedom of Information Act 2000. Unless the information is legally exempt from disclosure, the confidentiality of this e-mail and any replies cannot be guaranteed.

Any review, retransmission,dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipient is prohibited. If you received this in error, please contact the sender and delete the material from any system and destroy any copies.

We make every effort to keep our network free from viruses. However, it is your responsibility to ensure that this e-mail and any attachments are free of viruses as we can take no responsibility for any computer virus which might be transferred by way of this e-mail.

---

[aledj2]

I guess we could looking through all the samples on a run for each variant. Would any variant be present in multiple samples on a run? We'd still need a sample or run name for for the last two variants in the list.

[woook]

How many variants is in this list?

[aledj2]

105

[woook]

Can we feed the HGVS through mutalyzer?

---

From: Aled Jones notifications@github.com Sent: Tuesday, 13 November 2018 11:27 To: moka-guys/helpdesk Cc: woook; Comment Subject: Re: [moka-guys/helpdesk] List of variants for Ingenuity Verification (#342)

105

- You are receiving this because you commented. Reply to this email directly, view it on GitHubhttps://github.com/moka-guys/helpdesk/issues/342#issuecomment-438232876, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AFdGYqzgaDQZkJET1IT_MRl3DYKzbN61ks5uuqylgaJpZM4YQcdi.

---

This message may contain confidential information. If you are not the intended recipient please inform the sender that you have received the message in error before deleting it. Please do not disclose, copy or distribute information in this e-mail or take any action in relation to its contents. To do so is strictly prohibited and may be unlawful. Thank you for your co-operation.

NHSmail is the secure email and directory service available for all NHS staff in England and Scotland. NHSmail is approved for exchanging patient data and other sensitive information with NHSmail and other accredited email services.

For more information and to find out how you can switch, https://portal.nhs.net/help/joiningnhsmail

[aledj2]

Hi Rachael,

Would it be ok for all the variants to have the same/artificial data in the VCF, eg homozygous and call quality of 1000? (as per the WES VCF)

Would it be possible to provide the variants in a mutalyzer friendly format (transcript:HGVS).

Thanks, Aled

[rachaelmein]

Dear Aled

Yes all variants can have same artificial data in VCF. I have added a tab onto the excel file with variants in transcript:HGVS format P:\DNA LAB\Current\NGS worksheets\Ingenuity Panel Lists\Ingenuitys verification variants

Thanks very much

Rachael

From: Aled Jones [mailto:notifications@github.com] Sent: 14 November 2018 09:15 To: moka-guys/helpdesk helpdesk@noreply.github.com Cc: Mein Rachael Rachael.Mein@viapath.co.uk; Author author@noreply.github.com Subject: Re: [moka-guys/helpdesk] List of variants for Ingenuity Verification (#342)

Hi Rachael,

Would it be ok for all the variants to have the same/artificial data in the VCF, eg homozygous and call quality of 1000? (as per the WES VCF)

Would it be possible to provide the variants in a mutalyzer friendly format (transcript:HGVS).

Thanks, Aled

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttp://scanmail.trustwave.com/?c=8248&d=l-fr23zf3thnsz9Dy0RtuhWQDSznaOAVfp8ZOnASOA&u=https%3a%2f%2fgithub%2ecom%2fmoka-guys%2fhelpdesk%2fissues%2f342%23issuecomment-438591512, or mute the threadhttp://scanmail.trustwave.com/?c=8248&d=l-fr23zf3thnsz9Dy0RtuhWQDSznaOAVfspLbXcTbw&u=https%3a%2f%2fgithub%2ecom%2fnotifications%2funsubscribe-auth%2fAdw-G%5fkdi7OlsXhzzvdzH-Rsi9LFXF7mks5uu98YgaJpZM4YQcdi.

---

The information contained in this message and or attachments is intended only for the person or entity to which it is addressed and may contain confidential and/or privileged material. Unless otherwise specified, the opinions expressed herein do not necessarily represent those of Guy's and St Thomas' NHS Foundation Trust or any of its subsidiaries. The information contained in this e-mail may be subject to public disclosure under the Freedom of Information Act 2000. Unless the information is legally exempt from disclosure, the confidentiality of this e-mail and any replies cannot be guaranteed.

Any review, retransmission,dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipient is prohibited. If you received this in error, please contact the sender and delete the material from any system and destroy any copies.

We make every effort to keep our network free from viruses. However, it is your responsibility to ensure that this e-mail and any attachments are free of viruses as we can take no responsibility for any computer virus which might be transferred by way of this e-mail.

---

[aledj2]

Hi Rachael, I have the following errors when converting HGVS to chromosomal positions: NM_000152.4 could not be found - NM_000152.3 was suggested as an alternative NM_014625.3 could not be found - NM_014625.2 was suggested as an alternative NM_022068.3 could not be found - NM_022068.2 was suggested as an alternative NM_001267550.2 could not be found - NM_001267550.1 was suggested as an alternative

Line 88 had two HGVS descriptions, I assume the red one is the one to take?

[rachaelmein]

Those alternative transcript are fine. I must have missed the double entry on line 88. Yes the red one is correct.

Thanks very much. Rachael

From: Aled Jones [mailto:notifications@github.com] Sent: 04 December 2018 15:41 To: moka-guys/helpdesk helpdesk@noreply.github.com Cc: Mein Rachael Rachael.Mein@viapath.co.uk; Author author@noreply.github.com Subject: Re: [moka-guys/helpdesk] List of variants for Ingenuity Verification (#342)

Hi Rachael, I have the following errors when converting HGVS to chromosomal positions: NM_000152.4 could not be found - NM_000152.3 was suggested as an alternative NM_014625.3 could not be found - NM_014625.2 was suggested as an alternative NM_022068.3 could not be found - NM_022068.2 was suggested as an alternative NM_001267550.2 could not be found - NM_001267550.1 was suggested as an alternative

Line 88 had two HGVS descriptions, I assume the red one is the one to take?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttp://scanmail.trustwave.com/?c=8248&d=1Z-G3Fwy-U5v4sQ4_wKm6-2GY5Bxd0OT0VWDktkGPQ&u=https%3a%2f%2fgithub%2ecom%2fmoka-guys%2fhelpdesk%2fissues%2f342%23issuecomment-444145300, or mute the threadhttp://scanmail.trustwave.com/?c=8248&d=1Z-G3Fwy-U5v4sQ4_wKm6-2GY5Bxd0OT0VHVxdJSOQ&u=https%3a%2f%2fgithub%2ecom%2fnotifications%2funsubscribe-auth%2fAdw-G3PhEo8t2sPpZ9AQjK-eJW6lkhJEks5u1pd4gaJpZM4YQcdi.

---

The information contained in this message and or attachments is intended only for the person or entity to which it is addressed and may contain confidential and/or privileged material. Unless otherwise specified, the opinions expressed herein do not necessarily represent those of Guy's and St Thomas' NHS Foundation Trust or any of its subsidiaries. The information contained in this e-mail may be subject to public disclosure under the Freedom of Information Act 2000. Unless the information is legally exempt from disclosure, the confidentiality of this e-mail and any replies cannot be guaranteed.

Any review, retransmission,dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipient is prohibited. If you received this in error, please contact the sender and delete the material from any system and destroy any copies.

We make every effort to keep our network free from viruses. However, it is your responsibility to ensure that this e-mail and any attachments are free of viruses as we can take no responsibility for any computer virus which might be transferred by way of this e-mail.

---

[aledj2]

Hi Rachael, I have shared an Ingenuity analysis with you. How does it look?

[rachaelmein]

Thanks Aled It look good. All is present except for this one variant 10

16943450

CUBN

NM_001081.3

c.8071G>A

p.G2691R

NM_001081.3:c.8071G>A

I think you have put it in as chr1 instead of 10 as there is an extra variant.

Thanks very much for this.

Rachael

From: Aled Jones [mailto:notifications@github.com] Sent: 05 December 2018 11:56 To: moka-guys/helpdesk helpdesk@noreply.github.com Cc: Mein Rachael Rachael.Mein@viapath.co.uk; Author author@noreply.github.com Subject: Re: [moka-guys/helpdesk] List of variants for Ingenuity Verification (#342)

Hi Rachael, I have shared an Ingenuity analysis with you. How does it look?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttp://scanmail.trustwave.com/?c=8248&d=q7yH3P2qNNlIuClbvVB8PJXnqlWT9m87w5BsMNvBwQ&u=https%3a%2f%2fgithub%2ecom%2fmoka-guys%2fhelpdesk%2fissues%2f342%23issuecomment-444460357, or mute the threadhttp://scanmail.trustwave.com/?c=8248&d=q7yH3P2qNNlIuClbvVB8PJXnqlWT9m87w8NuM4jMlw&u=https%3a%2f%2fgithub%2ecom%2fnotifications%2funsubscribe-auth%2fAdw-G5JKthDNpPXiJwspd%5fYGxSSnYQTpks5u17RUgaJpZM4YQcdi.

---

The information contained in this message and or attachments is intended only for the person or entity to which it is addressed and may contain confidential and/or privileged material. Unless otherwise specified, the opinions expressed herein do not necessarily represent those of Guy's and St Thomas' NHS Foundation Trust or any of its subsidiaries. The information contained in this e-mail may be subject to public disclosure under the Freedom of Information Act 2000. Unless the information is legally exempt from disclosure, the confidentiality of this e-mail and any replies cannot be guaranteed.

Any review, retransmission,dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipient is prohibited. If you received this in error, please contact the sender and delete the material from any system and destroy any copies.

We make every effort to keep our network free from viruses. However, it is your responsibility to ensure that this e-mail and any attachments are free of viruses as we can take no responsibility for any computer virus which might be transferred by way of this e-mail.

---

[aledj2]

Have shared an updated analysis

[aledj2]

Hi Rachael, have you had a chance to look at this updated analysis? Do you need the vcf or are you just going to reanalyse the sample in ingenuity?

[rachaelmein]

Dear Aled

Sorry only just looked at the updated analysis. I will just use what you have sent me in Ingenuity so no need for anything further. Thanks so much for this, it’s a great help.

Cheers Rachael

From: Aled Jones [mailto:notifications@github.com] Sent: 18 December 2018 10:08 To: moka-guys/helpdesk helpdesk@noreply.github.com Cc: Mein Rachael Rachael.Mein@viapath.co.uk; Author author@noreply.github.com Subject: Re: [moka-guys/helpdesk] List of variants for Ingenuity Verification (#342)

Hi Rachael, have you had a chance to look at this updated analysis? Do you need the vcf or are you just going to reanalyse the sample in ingenuity?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttp://scanmail.trustwave.com/?c=8248&d=v8aY3AQbL1evZp7rYIlGOvaCPtf10lv0EJv85j-tkw&u=https%3a%2f%2fgithub%2ecom%2fmoka-guys%2fhelpdesk%2fissues%2f342%23issuecomment-448166428, or mute the threadhttp://scanmail.trustwave.com/?c=8248&d=v8aY3AQbL1evZp7rYIlGOvaCPtf10lv0EMv2tW3wmA&u=https%3a%2f%2fgithub%2ecom%2fnotifications%2funsubscribe-auth%2fAdw-GxQZ1Pecv%5f5NL1X4iRiFJJKc65%5fsks5u6L5ogaJpZM4YQcdi.

---

The information contained in this message and or attachments is intended only for the person or entity to which it is addressed and may contain confidential and/or privileged material. Unless otherwise specified, the opinions expressed herein do not necessarily represent those of Guy's and St Thomas' NHS Foundation Trust or any of its subsidiaries. The information contained in this e-mail may be subject to public disclosure under the Freedom of Information Act 2000. Unless the information is legally exempt from disclosure, the confidentiality of this e-mail and any replies cannot be guaranteed.

Any review, retransmission,dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipient is prohibited. If you received this in error, please contact the sender and delete the material from any system and destroy any copies.

We make every effort to keep our network free from viruses. However, it is your responsibility to ensure that this e-mail and any attachments are free of viruses as we can take no responsibility for any computer virus which might be transferred by way of this e-mail.

---

[aledj2]

Sample will be kept in Ingenuity. The original VCF can be found @ S:\Genetics_Data2\Array\Audits and Projects\181204_custompanel_ingenuity_verification