ROH output

[mcgml]

Hi,

I'm trying to identify regions of homozygosity in a single consanguineous sample. I used the command: bcftools roh -s sampleId -T BED VCF

Here's an example of the output:

1 762273 1 3.0 1 762472 1 19.8 1 876499 1 17.0 1 877715 1 22.6 1 877831 1 23.0 1 878314 1 25.6 1 879317 1 27.7 1 880238 1 27.9 1 880390 1 27.2

How can i convert these single positions into a range of homozygosity? Would removing low quality sites and applying something like circular binary segmentation do the job?

Thanks Matt

[pd3]

Take the whole region and use the average quality, for example like this https://gist.github.com/pd3/6ad82fdfffcd5afd4af6dcf804e6addd#file-roh-to-range

[mcgml]

Thank you!

Matt

From: pd3 [mailto:notifications@github.com] Sent: 22 June 2016 21:03 To: samtools/bcftools Cc: Matt Lyon (Cardiff and Vale UHB - Medical Genetics); Author Subject: Re: [samtools/bcftools] ROH output (#451)

Take the whole region and use the average quality, for example like this https://gist.github.com/pd3/6ad82fdfffcd5afd4af6dcf804e6addd#file-roh-to-range

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/samtools/bcftools/issues/451#issuecomment-227859913, or mute the threadhttps://github.com/notifications/unsubscribe/AMXTSluHtyKgI55JZvENdVpkgalsmSx9ks5qOZTkgaJpZM4I7n6h.

---

Confidentiality

This message is strictly confidential and intended for the person or organisation to whom it is addressed. If you are not the intended recipient of the message then please notify the sender immediately. Any of the statements or comments made above should be regarded as personal and not necessarily those of Cardiff & Vale University Health Board, any constituent part or connected body.

Email communication is subject to monitoring; for further information http://www.wales.nhs.uk/sitesplus/864/page/50329

Mae'r neges hon yn gyfrinachol. Os nad chi yw'r derbynnydd y bwriedid y neges
ar ei gyfer, byddwch mor garedig � rhoi gwybod
i'r anfonydd yn ddi-oed. Dylid ystyried unrhyw ddatganiadau neu sylwadau a wneir uchod yn rhai personol, ac nid o angenrhaid yn rhai o eiddo Bwrdd Iechyd Prifysgol
Caerdydd a�r Fro, nac unrhyw ran gyfansoddol ohoni na chorff cysylltiedig.

Mae cyfathrebu drwy e-bost yn amodol l fonitro; am fwy o wybodaeth. http://www.wales.nhs.uk/sitesplus/864/page/45247

Freedom of Information

Please be aware that, under the terms of the Freedom of Information Act 2000, Cardiff and Vale University Health Board may be required to make public the content of any emails or correspondence received.
For further information on Freedom of Information, please refer to the Cardiff and Vale UHB website http://www.cardiffandvaleuhb.wales.nhs.uk/freedom-of-information-new

Cofiwch fod yn ymwybodol ei bod yn bosibl
y bydd disgwyl i Bwrdd Iechyd Prifysgol Caerdydd a�r Fro roi cyhoeddusrwydd i gynnwys
unrhyw ebost neu ohebiaeth a dderbynnir, yn unol ag amodau'r Ddeddf Rhyddid Gwybodaeth 2000.
I gael mwy o wybodaeth am Ryddid Gwybodaeth, cofiwch gyfeirio at wefan Bwrdd Iechyd Prifysgol Caerdydd a�r Fro http://www.wales.nhs.uk/sitesplus/864/cymraeg

---

[rernst]

Just a note for people using the mentioned gist. There is a bug in the script that causes roh regions which contain only one roh position to be printed with a wrong end position (end of previous region).

Small example:

cat roh_ouput
X   130872087   1   6.5
X   130873045   1   4.8
X   130875051   0   99.0
X   130875936   1   1.8
X   130878582   1   3.5

cat roh_regions
X   130872087   130873045   1   5.7
X   130875051   130873045   0   99.0
X   130875936   130878582   1   2.6

[pd3]

Added a comment here https://gist.github.com/pd3/6ad82fdfffcd5afd4af6dcf804e6addd#gistcomment-1917861

[pd3]

The script is now updated. Note that with new versions of bcftools it should not be needed.