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mquinodo / AutoMap

Tool to find regions of homozygosity (ROHs) from sequencing data.
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common for a family #14

Closed mushalallam closed 2 years ago

mushalallam commented 2 years ago

Hi, I have WES VCFs for a family (father, mother and two kids ), those VCFs were generated using Illumina DRAGEN Bio-IT Platform, I used the Automap command as: bash AutoMap_v1.2.sh --vcf GN-21-0017.vcf,GN-21-0018.vcf,GN-21-0019.vcf,GN-21-0022.vcf --out family --genome hg19 --common I tried to change many AutoMap options however I usually get 0.00 Mb common ROH. As far as I understand I should get a common areas between them as they are one family. Could you please assist me to understand that, does the tool works with WES data? do I need to use ny own bed file? Thanks

mquinodo commented 2 years ago

Dear Mushalallam, Could you share the VCF file if possible so I can check it? Otherwise, can you share the complete output of the tool? Best, Mathieu

mushalallam commented 2 years ago

Hi Mathieu Thank you for your replay, attached are the complete output. Regards Mushal family.zip

mquinodo commented 2 years ago

Dear Mushal,

I meant the text output on the terminal.

Best, Mathieu

On Tue, 10 May 2022 at 08:57, Mushal Allam @.***> wrote:

Hi Mathieu Thank you for your replay, attached are the complete output. Regards Mushal http://url family.zip https://github.com/mquinodo/AutoMap/files/8659005/family.zip

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mushalallam commented 2 years ago

Hi Mathieu, Attached is the output from the terminal Thanks for all help family.txt

mquinodo commented 2 years ago

Dear Mushal,

The output is normal. There are just no common regions to the four individuals.

Best, Mathieu

On Wed, 11 May 2022 at 13:24, Mushal Allam @.***> wrote:

Hi Mathieu, Attached is the output from the terminal Thanks for all help family.txt https://github.com/mquinodo/AutoMap/files/8669456/family.txt

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mushalallam commented 2 years ago

Dear Mushal, The output is normal. There are just no common regions to the four individuals. Best, Mathieu … On Wed, 11 May 2022 at 13:24, Mushal Allam @.> wrote: Hi Mathieu, Attached is the output from the terminal Thanks for all help family.txt https://github.com/mquinodo/AutoMap/files/8669456/family.txt — Reply to this email directly, view it on GitHub <#14 (comment)>, or unsubscribe https://github.com/notifications/unsubscribe-auth/ALFFYMUIRWTIWXP2BZUSVE3VJOKIJANCNFSM5TYIYHUQ . You are receiving this because you commented.Message ID: @.>

Thanks Mathieu for all the investigations and help, how then you can explain that if they are family? Kind regards Mushal

mquinodo commented 1 year ago

Dear Mushal,

They are sharing alleles but not forcibly ROHs. This is completely normal. I would suggest you to read more about it: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1474039/#:~:text=Individuals%20born%20of%20consanguineous%20union,recessive%20disease%20within%20these%20sibships .

Best, Mathieu

On Thu, 12 May 2022 at 09:40, Mushal Allam @.***> wrote:

Dear Mushal, The output is normal. There are just no common regions to the four individuals. Best, Mathieu … <#m9032333991084338022> On Wed, 11 May 2022 at 13:24, Mushal Allam @.> wrote: Hi Mathieu, Attached is the output from the terminal Thanks for all help family.txt https://github.com/mquinodo/AutoMap/files/8669456/family.txt https://github.com/mquinodo/AutoMap/files/8669456/family.txt — Reply to this email directly, view it on GitHub <#14 (comment) https://github.com/mquinodo/AutoMap/issues/14#issuecomment-1123606678>, or unsubscribe https://github.com/notifications/unsubscribe-auth/ALFFYMUIRWTIWXP2BZUSVE3VJOKIJANCNFSM5TYIYHUQ https://github.com/notifications/unsubscribe-auth/ALFFYMUIRWTIWXP2BZUSVE3VJOKIJANCNFSM5TYIYHUQ . You are receiving this because you commented.Message ID: @.>

Thanks Mathieu for all the investigations and help, how then you can explain that if they are family? Kind regards Mushal

— Reply to this email directly, view it on GitHub https://github.com/mquinodo/AutoMap/issues/14#issuecomment-1124640123, or unsubscribe https://github.com/notifications/unsubscribe-auth/ALFFYMVJTCCICS3QPH6ESHTVJSYX3ANCNFSM5TYIYHUQ . You are receiving this because you commented.Message ID: @.***>