Gedmatch calculators on Vahaduo

Quote:

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Originally Posted by vbnetkhio

then it's probably hg18, which isn't offered here..

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Maybe, but even one snp wasn't converted?

Quote:

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Originally Posted by Lucas

Maybe, but even one snp wasn't converted?

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maybe that's how it is with bams.

can you check this?
http://genometoolbox.blogspot.com/20...8-or-hg19.html

edit:
or this, if there's no header:

Code:

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samtools view filename.bam | head -n 5

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Quote:

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Originally Posted by vbnetkhio

maybe that's how it is with bams.

can you check this?
http://genometoolbox.blogspot.com/20...8-or-hg19.html

edit:
or this, if there's no header:

Code:

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samtools view filename.bam | head -n 5

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samtools view -H filename.bam
This command should show only header, but it shows thousands lines and I'm still waiting for end of this shit:)

This shows me this:)
https://i.imgur.com/KnpsWVW.png

Quote:

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Originally Posted by Lucas

samtools view -H filename.bam
This command should show only header, but it shows thousands lines and I'm still waiting for end of this shit:)

This shows me this:)
https://i.imgur.com/KnpsWVW.png

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could this actually be fastq files, labelled as BAM?

fastq files have lines like this (with the "HWUSI", etc.)
https://en.wikipedia.org/wiki/FASTQ_...ce_identifiers

Quote:

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Originally Posted by vbnetkhio

could this actually be fastq files, labelled as BAM?

fastq files have lines like this (with the "HWUSI", etc.)
https://en.wikipedia.org/wiki/FASTQ_...ce_identifiers

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Yes.... possible:) Those who made it are not the smartest ones geneticists.

Quote:

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Originally Posted by Lucas

Yes.... possible:) Those who made it are not the smartest ones geneticists.

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they are in hg19 according to the study. did you try running them trough fastq to bam?

Quote:

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Originally Posted by Lucas

Yes.... possible:) Those who made it are not the smartest ones geneticists.

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Are you implying they're not Slavs

@Lucas,
You've ignored me for some reason but I'm trying to unify the name on Dodecad K12b 'cause there is an unnecessary discrepancy going on there.
Please delete these:
Iran_Arab, Iraqi_Arab, Lur_Iran, Iraqi_Turkmen, Iran_Bandari, Iran_Mazandaran, Iran_Khorasan, Yagnobi
and replace them with these:

Code:

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Arab_Iran,18.52,0.29,2.61,0.21,6.69,3.63,4.18,3.35,23.35,0.45,34.63,1.87
Arab_Iraq,16.56,0.45,2.95,0.27,8.15,3,3.31,3.67,25.43,0.78,33.56,1.82
Iranian_Bandari,35.42,0.33,0.37,0.70,2.01,6.42,11.00,1.81,11.25,0.00,25.24,5.46
Iranian_Khorasan,28.01,1.89,0.34,0.29,6.34,9.65,7.63,0.44,10.14,2.84,32.17,0.26
Iranian_Lur,27.78,1.32,0.8,0.37,6.35,4.08,4.03,0.5,14.64,0.61,39.33,0.2
Iranian_Mazandaran,33.07,0.48,0.25,0.26,2.86,5.68,5.27,0.32,10.96,0.26,40.38,0.19
Turkmen_Iraq,21.88,1.97,1.20,0.49,7.52,5.40,4.10,0.79,16.48,1.12,38.44,0.59
Yaghnobi_Tajikistan,30.81,3.92,0,0.44,7.54,22.11,5.62,0,4.15,2.22,23.18,0

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(Yaghnobi is also recalculated, so it's a tiny bit different)

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Adding the Russian average is up to you.

Quote:

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Originally Posted by Leto

@Lucas,
You've ignored me for some reason but I'm trying to unify the name on Dodecad K12b 'cause there is an unnecessary discrepancy going on there.
Please delete these:
Iran_Arab, Iraqi_Arab, Lur_Iran, Iraqi_Turkmen, Iran_Bandari, Iran_Mazandaran, Iran_Khorasan, Yagnobi
and replace them with these:

Code:

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Arab_Iran,18.52,0.29,2.61,0.21,6.69,3.63,4.18,3.35,23.35,0.45,34.63,1.87
Arab_Iraq,16.56,0.45,2.95,0.27,8.15,3,3.31,3.67,25.43,0.78,33.56,1.82
Iranian_Bandari,35.42,0.33,0.37,0.70,2.01,6.42,11.00,1.81,11.25,0.00,25.24,5.46
Iranian_Khorasan,28.01,1.89,0.34,0.29,6.34,9.65,7.63,0.44,10.14,2.84,32.17,0.26
Iranian_Lur,27.78,1.32,0.8,0.37,6.35,4.08,4.03,0.5,14.64,0.61,39.33,0.2
Iranian_Mazandaran,33.07,0.48,0.25,0.26,2.86,5.68,5.27,0.32,10.96,0.26,40.38,0.19
Turkmen_Iraq,21.88,1.97,1.20,0.49,7.52,5.40,4.10,0.79,16.48,1.12,38.44,0.59
Yaghnobi_Tajikistan,30.81,3.92,0,0.44,7.54,22.11,5.62,0,4.15,2.22,23.18,0

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(Yaghnobi is also recalculated, so it's a tiny bit different)

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Adding the Russian average is up to you.

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No, I was just busy. Added:)

Quote:

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Originally Posted by Lucas

No, I was just busy. Added:)

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Now there are 2 identical averages with different names in it
Lur_Iran and Iranian_Lur (for naming purposes you should remove Lur_Iran)
Edit: same for Arab_Iraq and Iraq_arab