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Steven-N-Hart / vcf-miner

VCF-Miner: A graphical user interface for sorting, filtering and querying annotated VCF Files
MIT License
37 stars 11 forks source link

vcf-miner with ped files? #2

Closed ramaniak closed 7 years ago

ramaniak commented 8 years ago

Hello, If I understand correctly, vcf-miner does not utilize pedigree information to filter for variants. Is this correct? If so, is there any development in progress that would see this implemented in future releases?

thanks very much Arun

Steven-N-Hart commented 8 years ago

Arun, Can you describe the feature a little bit more that you are requesting? You should be allowed to filter by different combinations of samples - even without a PED file.

ramaniak commented 8 years ago

Hello Steven, Thanks for your quick response. I am looking to carry out analysis with trios: denovo calling, compound heterozygotes and such. Is there a way to carry this out in the current release?

thanks

On Tue, Jun 21, 2016 at 5:03 PM, Steven N Hart notifications@github.com wrote:

Arun, Can you describe the feature a little bit more that you are requesting? You should be allowed to filter by different combinations of samples - even without a PED file.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/Steven-N-Hart/vcf-miner/issues/2#issuecomment-227571102, or mute the thread https://github.com/notifications/unsubscribe/AFzoBpnWXTR4dTRXXMi8LP1iAaUIAfJVks5qOFGggaJpZM4I7J1Z .

Steven-N-Hart commented 8 years ago

Yes.
To get de novo: create a group for the parents And 1 for the Child. In the Custom Tab of the filter modal, select "Variants NOT IN Group", with the "Either" radio button selected where the value = "Parents". This removes any variant found in mom OR dad - hence de novo.

For compound het, select "Variants IN Group" = "Parent", but this time select heterozygous. Next add another filter where "Variants IN Group" = "Child" and set the genotype to "Heterozygous". Now, to get true compound hets - assuming neither parent has the disease, you would further select " "Variants NOT IN Group" = "Parent" but select "Homozygous" (remove variants that are homozygous in either parent)

Make sense?

ramaniak commented 8 years ago

Yes, makes sense. Let me try it out and let you know of I run into any difficulties.

Cheers Arun

On Tuesday, June 21, 2016, Steven N Hart notifications@github.com wrote:

Yes.

To get de novo: create a group for the parents And 1 for the Child. In the Custom Tab of the filter modal, select "Variants NOT IN Group", with the "Either" radio button selected where the value = "Parents". This removes any variant found in mom OR dad - hence de novo.

For compound het, select "Variants IN Group" = "Parent", but this time select heterozygous. Next add another filter where "Variants IN Group" = "Child" and set the genotype to "Heterozygous". Now, to get true compound hets - assuming neither parent has the disease, you would further select " "Variants NOT IN Group" = "Parent" but select "Homozygous" (remove variants that are homozygous in either parent)

Make sense?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/Steven-N-Hart/vcf-miner/issues/2#issuecomment-227575907, or mute the thread https://github.com/notifications/unsubscribe/AFzoBqFRsXYchuDWtO3bXmKJ6I6ft1DKks5qOFW0gaJpZM4I7J1Z .