Comments (6)
laninsky
commented on July 27, 2024
Hiya Ludo,
Thanks for lodging this issue - can I grab your popmap.txt file off you too? https://github.com/laninsky/GBS_SNP_filter#popmaptxt
Ta!
Alana
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ldutoit
commented on July 27, 2024
yes of course!
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laninsky
commented on July 27, 2024
Thanks Ludo - you've indeed found a bug in how the code handles "./." when the coverage of 0 is not explicitly given. I will do my best to fix this tomorrow and let you know :)
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ldutoit
commented on July 27, 2024
no worries at all, nor emergency!
I hope it helps your code.
Cheers
Ludo
…On Wed, 10 Apr 2019 at 15:31, Alana Alexander ***@***.***> wrote:
Thanks Ludo - you've indeed found a bug in how the code handles "./." when
the coverage of 0 is not explicitly given. I will do my best to fix this
tomorrow and let you know :)
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laninsky
commented on July 27, 2024
Kia ora Ludo - think I've fixed this (and a few other 'knock on' issues the fix caused :P ), and the new code now seems to be working on your dataset. However, your GBS_SNP_filter.txt file would also need to be tweaked a little to something along the lines of the following (rather than the seven line file you sent me originally):
test.vcf
0.0
1
0.05
0.5
1
#CHROM
I've added in a check to make sure that folks have enough stuff in GBS_SNP_filter.txt so hopefully this will fail at the beginning rather than half-way through in the future :) Let me know if the readme needs some more work on describing how to set up the GBS_SNP_filter.txt file, otherwise if it now seems to be working on your 'proper' dataset, let me know and I'll close this issue.
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ldutoit
commented on July 27, 2024
great thanks, super awesome sweet stuff!
Ludo
…On Thu, 11 Apr 2019 at 16:46, Alana Alexander ***@***.***> wrote:
Kia ora Ludo - think I've fixed this (and a few other 'knock on' issues
the fix caused :P ), and the new code now seems to be working on your
dataset. However, your GBS_SNP_filter.txt file would also need to be
tweaked a little to something along the lines of the following (rather than
the seven line file you sent me originally):
test.vcf
0.0
1
0.05
0.5
1
#CHROM
I've added in a check to make sure that folks have enough stuff in
GBS_SNP_filter.txt so hopefully this will fail at the beginning rather than
half-way through in the future :) Let me know if the readme needs some more
work on describing how to set up the GBS_SNP_filter.txt file, otherwise if
it now seems to be working on your 'proper' dataset, let me know and I'll
close this issue.
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You are receiving this because you authored the thread.
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<#3 (comment)>,
or mute the thread
<https://github.com/notifications/unsubscribe-auth/AELGAbcbIqtp9GWDgeRnmtOHZOb9MkNGks5vfr43gaJpZM4clz4e>
.
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Related Issues (9)
- Error in -removepops HOT 14
- Address some deprecating in code HOT 1
- ld performance in the package HOT 2
- Error in generating .HWE.vcf file HOT 4
- Failing after PLINK for stickleback test data HOT 1
- Add some guidance on what vcf to use
- Error in generating the .ld.vcf file (the final step) HOT 4
- Check the formatting of the vcf
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