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Sunday, December 18, 2016. What can we learn from one Y chromosome? Some time ago I became interested in chromosome Y. It all started from my maternal grandfather. He was born in Lauria, a small town in the south of Italy. After the civil records for Lauria became available online, it was pretty easy to reconstruct his family tree all the way to the 18th century. However, as shown in the following diagram, one small piece was missing (at the top right):. And that holds only for point mutations. To my gra...

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genetics for fun | apol1.blogspot.com Reviews

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Sunday, December 18, 2016. What can we learn from one Y chromosome? Some time ago I became interested in chromosome Y. It all started from my maternal grandfather. He was born in Lauria, a small town in the south of Italy. After the civil records for Lauria became available online, it was pretty easy to reconstruct his family tree all the way to the 18th century. However, as shown in the following diagram, one small piece was missing (at the top right):. And that holds only for point mutations. To my gra...

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genetics for fun | apol1.blogspot.com Reviews

https://apol1.blogspot.com

Sunday, December 18, 2016. What can we learn from one Y chromosome? Some time ago I became interested in chromosome Y. It all started from my maternal grandfather. He was born in Lauria, a small town in the south of Italy. After the civil records for Lauria became available online, it was pretty easy to reconstruct his family tree all the way to the 18th century. However, as shown in the following diagram, one small piece was missing (at the top right):. And that holds only for point mutations. To my gra...

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genetics for fun: What can we learn from one Y chromosome?

http://apol1.blogspot.com/2016/12/what-can-we-learn-from-one-y-chromosome.html

Sunday, December 18, 2016. What can we learn from one Y chromosome? Some time ago I became interested in chromosome Y. It all started from my maternal grandfather. He was born in Lauria, a small town in the south of Italy. After the civil records for Lauria became available online, it was pretty easy to reconstruct his family tree all the way to the 18th century. However, as shown in the following diagram, one small piece was missing (at the top right):. And that holds only for point mutations. To my gra...

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genetics for fun: May 2015

http://apol1.blogspot.com/2015_05_01_archive.html

Tuesday, May 19, 2015. Annotate CpG mutations in a VCF file. T, while the second kind shows as a A. T But distinguishing CpG transitions from non-CpG transitions within a VCF is not possible without additional information as we need information about the sequence context. Now that we have our VCF file with all CpG mutations, we can use SnpSift to annotate our input VCF file. I selected SnpSift because it is quite fast and flexible compared to other tools like bcftools (see here. Install latest version of...

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genetics for fun: November 2013

http://apol1.blogspot.com/2013_11_01_archive.html

Monday, November 18, 2013. There are a lot of interesting analyses that segments inherited identical-by-descent (IBD) can be informative for. However, it takes some steps to setup a fully functional IBD pipeline. Here is a basic one that will work with any dataset in binary plink format. It will first phase the data with hapi-ur, then detect IBD segments using beagle, and finally detect clusters of IBD individuals using dash. To begin with, you need to setup a few variables:. Subscribe to: Posts (Atom).

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genetics for fun: May 2014

http://apol1.blogspot.com/2014_05_01_archive.html

Tuesday, May 13, 2014. How do I identify all the homopolymer run indels in a VCF file? Input="$1" # input VCF file in any format accepted by bcftools. Ref="$2" # reference genome in fasta format. Bcftools view -HG $input cut -f1-5 awk '$4! ACGT]($ ,)" $5! Awk '{print $1" t"$2 length($4)-1" t"$2 length($4) 5" t"$3}'. Bedtools getfasta -name -fi $ref -bed /dev/stdin -fo /dev/stdout. Awk 'NR%2= 1 {printf substr($0,2)" t"} NR%2= 0'. Grep "AAAAAA$ CCCCCC$ GGGGGG$ TTTTTT$" cut -f1 sort.

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genetics for fun: Best practice for converting VCF files to plink format

http://apol1.blogspot.com/2014/11/best-practice-for-converting-vcf-files.html

Tuesday, November 25, 2014. Best practice for converting VCF files to plink format. There is no way to tell, as the plink format does not record this information. Keeping this in mind, we are going to need two pieces of software for the conversion, bcftools and plink2. Here how to install them:. We are also going to need a copy of the GRCh37 reference. If you don't have this, it will take a while to download, but it can be done with the following commands:. Bcftools norm -Ou -m -any input.vcf.gz ...Usual...

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apol1.blogspot.com

genetics for fun

Sunday, December 18, 2016. What can we learn from one Y chromosome? Some time ago I became interested in chromosome Y. It all started from my maternal grandfather. He was born in Lauria, a small town in the south of Italy. After the civil records for Lauria became available online, it was pretty easy to reconstruct his family tree all the way to the 18th century. However, as shown in the following diagram, one small piece was missing (at the top right):. And that holds only for point mutations. To my gra...

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