Gedmatch calculators on Vahaduo

[Lucas]

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

Maybe, but even one snp wasn't converted?

[vbnetkhio]

Maybe, but even one snp wasn't converted?

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:

samtools view filename.bam | head -n 5

[Lucas]

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:

samtools view filename.bam | head -n 5

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

[vbnetkhio]

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

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

[Lucas]

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

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

[vbnetkhio]

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

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

[Dick]

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

Are you implying they're not Slavs

[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:

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

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

- - - - - -

Adding the Russian average is up to you.

[Lucas]

@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:

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

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

- - - - - -

Adding the Russian average is up to you.

No, I was just busy. Added

[Dr_Maul]

No, I was just busy. Added

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