DReichLab / DReichLab/AdmixTools
bad chrom error - fstats
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Description
Dear all,
I have been trying to used Admixtools to calculate fstatistics between several individuals. I have two questions concerning the runs:
- can I calculate the fstats for species instead of individuals? DO I set it up in the .ind file, changing the POP column for each species name?
- I am using capture sequence data and the reference used to map the reads is a set of contigs, so when I try to run the analysis I get this error:
fatalx:
bad chrom: 625_mc1r
Aborted
Is there any option I can use to accept the different "chromosome" names I have in my files?
Thanks in advance!
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- Read the whole issue, then the project's contributing guide.
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Research direction
Start by reviewing how AdmixTools reads the .ind POP column and validates chromosome names, then reproduce the run using the contig name "625_mc1r" and the capture-sequence inputs described here. Done means determining whether species-level grouping and nonstandard contig names are supported, and documenting the required input or the needed change.
Written by the indexing model from the issue text.
Assessment
- Domain
- bioinformatics
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100