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Conversion of VCF file
#1
Greetings for new BIG Y order. I believe results will be very interesting.

BTW, can someone explain to me how to open the VCF on the link: https://drive.google.com/file/d/1jzGm2xU...sp=sharing

Actually, I have never analyzed it but would like to try.
 
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#2
You can open the VCF with any text editor.
mtDNA: T2f2
Y-DNA: R1b1a1a2a2c1a1a3 (A1777/BY611/Y10789)
 
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#3
(06-16-2018, 09:26 PM)Trifud Писа: You can open the VCF with any text editor.

Thank you for help.
I am too inexperienced in this when I open it in notepad or word it is a mess.
 
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#4
No, it is not a mess. In the beginning of the VCF you have the key to how it is structured. Most important fields are 
CHROM which should be chrY, POS which gives you the coordinate on the chromosome according to the reference genome used (which you have listed in the beginning - ##reference=ucsc.hg38.fasta), REF which gives you the reference allele in the reference genome, ALT which gives you the allele in the sample if different from the reference or a dot if the same, QUAL which gives you the quality and the last two columns which give you statistical information and the key to it. Consider this line:


Код:
chrY 16643399 . G A 1484.13 PASS BQ=35.8089;GC=0.51475;HL=2;HR=1.5;IndelCnt=0;MQ=60;MQ0=0;MismatchCnt=0 GT:AD:DP:GQ:PL:AB:SR:BQ:LowMQ:ClipCnt:ReadOffset:RAD:AS 1/1:0,124:124:5000:500,500,0:1:0.556452:35:0,0:0,5:0,74.4597:0,55:0,123.967


It tells you that the sample has a mutation from G to A at position 16643399 on the Y chromosome based on 124 A reads and 0 G reads with mean quality of 1484.13 (among other data). This mutation corresponds to SNP CTS9219: http://ybrowse.y-chromosome.org/gb2/gbro...3Adatabase
mtDNA: T2f2
Y-DNA: R1b1a1a2a2c1a1a3 (A1777/BY611/Y10789)
 
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#5
(06-17-2018, 12:17 AM)Trifud Писа: No, it is not a mess. In the beginning of the VCF you have the key to how it is structured. Most important fields are 
CHROM which should be chrY, POS which gives you the coordinate on the chromosome according to the reference genome used (which you have listed in the beginning - ##reference=ucsc.hg38.fasta), REF which gives you the reference allele in the reference genome, ALT which gives you the allele in the sample if different from the reference or a dot if the same, QUAL which gives you the quality and the last two columns which give you statistical information and the key to it. Consider this line:


Код:
chrY 16643399 . G A 1484.13 PASS BQ=35.8089;GC=0.51475;HL=2;HR=1.5;IndelCnt=0;MQ=60;MQ0=0;MismatchCnt=0 GT:AD:DP:GQ:PL:AB:SR:BQ:LowMQ:ClipCnt:ReadOffset:RAD:AS 1/1:0,124:124:5000:500,500,0:1:0.556452:35:0,0:0,5:0,74.4597:0,55:0,123.967


It tells you that the sample has a mutation from G to A at position 16643399 on the Y chromosome based on 124 A reads and 0 G reads with mean quality of 1484.13 (among other data). This mutation corresponds to SNP CTS9219: http://ybrowse.y-chromosome.org/gb2/gbro...3Adatabase

Thank you Trifud! I do not know what problem with my notepad is, but I opened it in Excel and looks perfect and easy for analysis.
 
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#6
The line breaks in the VCF could be UNIX-style.
mtDNA: T2f2
Y-DNA: R1b1a1a2a2c1a1a3 (A1777/BY611/Y10789)
 
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#7
(06-19-2018, 12:45 PM)Trifud Писа: The line breaks in the VCF could be UNIX-style.

Maybe it is something with my text editor settings.
Anyway, it is easier for me to manipulate and analyze data if it is in Excel.
Ybrowse.org r is based on hg38, while data in the study are hg37. I suppose there are differences in positions, am I right?
 
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#8
Yes, you can use LiftOver to convert the coordinates: https://genome.ucsc.edu/cgi-bin/hgLiftOver
mtDNA: T2f2
Y-DNA: R1b1a1a2a2c1a1a3 (A1777/BY611/Y10789)
 
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#9
(06-19-2018, 06:14 PM)Trifud Писа: Yes, you can use LiftOver to convert the coordinates: https://genome.ucsc.edu/cgi-bin/hgLiftOver
How to prepare input data? I have tried several times and always get an error.
Sorry for so many questions, and thanks a lot for your help.
 
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#10
(06-19-2018, 07:30 PM)Влад Писа:
(06-19-2018, 06:14 PM)Trifud Писа: Yes, you can use LiftOver to convert the coordinates: https://genome.ucsc.edu/cgi-bin/hgLiftOver
How to prepare input data? I have tried several times and always get an error.
Sorry for so many questions, and thanks a lot for your help.

Actually, I think it works in described format chr1:16039660-16039660
I did not see field View Conversions
 
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