af-dist plugin output query
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Assessment
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Newbie friendliness
- 20/100
- Issue type
- Bug
- Clarity
- Needs clarification
- Activity status
- Stale
- Domain
- bioinformatics
Research direction
Start with the +af-dist how-to and the reported data.dist.txt output; obtain the exact command and VCF details needed to reproduce it. Compare the plugin's expected input with the all-zero fourth column, then document the cause or confirm a plugin issue. If the plotting request is in scope, add the R or Python scripts for the linked page's figures.
Written by the indexing model from the issue text.
Description
Hi,
While attempting to check allele Frequency with 1000g using the +af-dist plugin, i got this output
[msr52@login-e-10 v1_chip_extra]$ head data.dist.txt
PROB_DIST 0.000000 0.100000 0
PROB_DIST 0.100000 0.200000 0
PROB_DIST 0.200000 0.300000 0
PROB_DIST 0.300000 0.400000 0
PROB_DIST 0.400000 0.500000 0
PROB_DIST 0.500000 0.600000 0
PROB_DIST 0.600000 0.700000 0
PROB_DIST 0.700000 0.800000 0
PROB_DIST 0.800000 0.900000 0
PROB_DIST 0.900000 1.000000 0
In the 4th column, all I see is zeros. I was expecting some numbers. Wondering what is wrong with my VCF files?
Is it possible to share R or python codes for the pictures available on this page
available here http://samtools.github.io/bcftools/howtos/plugin.af-dist.html?
- Dominant language
- C
- Stars
- 891
- Forks
- 277
- Avg merge
- 2d 23h
- Merged PRs (30d)
- 2
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