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  #1  
Old 14th April 2018, 01:08 PM
singingfalls singingfalls is offline
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Join Date: Dec 2014
Location: Oregon, USA
Posts: 109
Hg38

It is my understanding that there is a switch taking place from hg19 to hg38. How do I ascertain if my file is hg38?
I had Big Y done in 2015.
Apologies if this has already been asked. I did a search with no results that I can find.
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  #2  
Old 15th April 2018, 12:56 AM
dna dna is offline
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Posts: 2,963
It is my understanding that for BAM (Binary Alignment Map) files the answer is simple. FTDNA does not provide hg38 BAM files yet. Everybody, who has one, has a hg19 BAM.

On the other hand, FTDNA has switched VCF (Variant Call Format) files to hg38, last year. But you do not have to guess based on the file date.

FTDNA provides VCF file in a ZIP archive containing the following three files
  • readme.txt ( that file contains misleading information, please ignore it )
  • regions.bed
  • variants.vcf
Luckily for us, variants.vcf is a human readable file. So copy it from the ZIP to, for example, your desktop.

Unfortunately, Microsoft Windows would think that it is a vCard visiting card type of a file (Virtual Contact File), so you cannot just open it. However, you can open a Notepad and drag your VCF file into it. Since, as far as Notepad is concerned, the entire VCF file is one single line, you may need to wait some time before the contents get displayed.

An old style file would start with something like
##fileformat=VCFv4.1##fileDate=20150607##FORMAT=<I D=GT,Number=1,Type=String,Description="Genotype"># #contig=<ID=chrY,length=59876543,assembly=hg19>
A new one would start like
##fileformat=VCFv4.1##fileDate=20170809##reference =ucsc.hg38.fasta


Mr. W.


P.S.
According to a post from 2018-04-09 http://forums.familytreedna.com/showthread.php?p=450578 FTDNA support volunteered the following:
"Right now the current time frame for BAM files to be produced again is middle of May. I apologize for the inconvenience."

Last edited by dna; 15th April 2018 at 01:06 AM.
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  #3  
Old 15th April 2018, 01:07 AM
singingfalls singingfalls is offline
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Join Date: Dec 2014
Location: Oregon, USA
Posts: 109
My gratitude sir. I do have the hg38 VCF file and will patiently for the updated BAM file.

All the best.

Stan
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  #4  
Old 16th April 2018, 12:30 PM
dtvmcdonald dtvmcdonald is offline
mtDNA: | Big Y Pending
 
Join Date: Mar 2011
Posts: 264
Excel will read VCF and BED files
without the "one line" problem of Notepad.

Last edited by dtvmcdonald; 16th April 2018 at 12:34 PM.
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  #5  
Old 16th April 2018, 06:06 PM
dna dna is offline
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Join Date: Aug 2014
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Quote:
Originally Posted by dtvmcdonald View Post
Excel will read VCF and BED files
without the "one line" problem of Notepad.
Thank you for the excellent tip!


Mr. W.
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  #6  
Old 18th April 2018, 09:35 AM
rrtipton1 rrtipton1 is offline
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Join Date: Oct 2006
Location: Crossville, TN
Posts: 15
If all you want to know is whether a VCF file is hg38 or hg19, you should be able to tell by just looking at the file name. The hg19 files had names beginning with the characters “bigy-“ while the hg38 files star with “bigy2-“.
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