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szpiech / selscan

Haplotype based scans for selection
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norm across the genome #74

Closed sadiexiaoyu closed 2 years ago

sadiexiaoyu commented 2 years ago

Hi, Szpiech,

I would like to ask if I norm the iHS results across the genome, do I have to norm all chromosomes (except X and Y) at the same time? e.g., norm --ihs --files chr1_African.ihs.out chr2_African.ihs.out chr3_African.ihs.out chr4_African.ihs.out chr5_African.ihs.out chr6_African.ihs.out chr7_African.ihs.out chr8_African.ihs.out chr9_African.ihs.out chr10_African.ihs.out chr11_African.ihs.out chr12_African.ihs.out chr13_African.ihs.out chr14_African.ihs.out chr15_African.ihs.out chr16_African.ihs.out chr17_African.ihs.out chr18_African.ihs.out chr19_African.ihs.out chr20_African.ihs.out chr21_African.ihs.out chr22_African.ihs.out

szpiech commented 2 years ago

Hi,

Yes the autosomes should be normalized together.

Zachary

Le mer. 16 mars 2022 à 10:20 AM, sadiexiaoyu @.***> a écrit :

Hi, Szpiech,

I would like to ask if I norm the iHS results across the genome, do I have to norm all chromosomes (except X and Y) at the same time? e.g., norm --ihs --files chr1_African.ihs.out chr2_African.ihs.out chr3_African.ihs.out chr4_African.ihs.out chr5_African.ihs.out chr6_African.ihs.out chr7_African.ihs.out chr8_African.ihs.out chr9_African.ihs.out chr10_African.ihs.out chr11_African.ihs.out chr12_African.ihs.out chr13_African.ihs.out chr14_African.ihs.out chr15_African.ihs.out chr16_African.ihs.out chr17_African.ihs.out chr18_African.ihs.out chr19_African.ihs.out chr20_African.ihs.out chr21_African.ihs.out chr22_African.ihs.out

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sadiexiaoyu commented 2 years ago

Hi, Yes the autosomes should be normalized together. Zachary Le mer. 16 mars 2022 à 10:20 AM, sadiexiaoyu @.> a écrit : … Hi, Szpiech, I would like to ask if I norm the iHS results across the genome, do I have to norm all chromosomes (except X and Y) at the same time? e.g., norm --ihs --files chr1_African.ihs.out chr2_African.ihs.out chr3_African.ihs.out chr4_African.ihs.out chr5_African.ihs.out chr6_African.ihs.out chr7_African.ihs.out chr8_African.ihs.out chr9_African.ihs.out chr10_African.ihs.out chr11_African.ihs.out chr12_African.ihs.out chr13_African.ihs.out chr14_African.ihs.out chr15_African.ihs.out chr16_African.ihs.out chr17_African.ihs.out chr18_African.ihs.out chr19_African.ihs.out chr20_African.ihs.out chr21_African.ihs.out chr22_African.ihs.out — Reply to this email directly, view it on GitHub <#74>, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABAKRQVDFTFTUHE42DV4SJTVAHUZNANCNFSM5Q4BFDDA . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub. You are receiving this because you are subscribed to this thread.Message ID: @.>

Thank you! And I would like to ask, is there any way to calculate the proportion of SNPs with abs iHS>2 in a 51 SNPs window? I only found --winsize in the norm script. Or should I calculate it by myself?

szpiech commented 2 years ago

I thought I had replied to this, sorry if it did not come through.

Unfortunately I haven't implemented a snp-based window method for norm, but it is certainly a good addition to make.

sadiexiaoyu commented 2 years ago

Thank you!

szpiech commented 1 year ago

Hi,

Unfortunately I haven't implemented a snp-based window method for norm, but it is certainly a good addition to make.

-Zachary

On Wed, Mar 16, 2022 at 11:01 AM sadiexiaoyu @.***> wrote:

Hi, Yes the autosomes should be normalized together. Zachary Le mer. 16 mars 2022 à 10:20 AM, sadiexiaoyu @.

> a écrit : … <#m-7395047794121312839> Hi, Szpiech, I would like to ask if I norm the iHS results across the genome, do I have to norm all chromosomes (except X and Y) at the same time? e.g., norm --ihs --files chr1_African.ihs.out chr2_African.ihs.out chr3_African.ihs.out chr4_African.ihs.out chr5_African.ihs.out chr6_African.ihs.out chr7_African.ihs.out chr8_African.ihs.out chr9_African.ihs.out chr10_African.ihs.out chr11_African.ihs.out chr12_African.ihs.out chr13_African.ihs.out chr14_African.ihs.out chr15_African.ihs.out chr16_African.ihs.out chr17_African.ihs.out chr18_African.ihs.out chr19_African.ihs.out chr20_African.ihs.out chr21_African.ihs.out chr22_African.ihs.out — Reply to this email directly, view it on GitHub <#74 https://github.com/szpiech/selscan/issues/74>, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABAKRQVDFTFTUHE42DV4SJTVAHUZNANCNFSM5Q4BFDDA https://github.com/notifications/unsubscribe-auth/ABAKRQVDFTFTUHE42DV4SJTVAHUZNANCNFSM5Q4BFDDA . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub. You are receiving this because you are subscribed to this thread.Message ID: @.>

Thank you! And I would like to ask, is there any way to calculate the proportion of SNPs with abs iHS>2 in a 51 SNPs window? I only found --winsize in the norm script. Or should I calculate it by myself?

— Reply to this email directly, view it on GitHub https://github.com/szpiech/selscan/issues/74#issuecomment-1069222934, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABAKRQQRNIWRZCFKDNTIZX3VAHZUXANCNFSM5Q4BFDDA . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

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