Hi all,
Does anybody understand how the --LROH option works in vcf tools? It is designed to detect long runs of homozygosity, which is exactly what I want to do, but without knowing more about the underlying assumptions it makes I am hesitant to use it. There is no clear explanation of how to interpret the output files. Any help or pointers greatly appreciated. Thank you in advance.
Cheers,
Rubal
1 answer
The LROH option implements the algorithm described in Auton et al., Genome Research, 2009, although using the Forward-backwards algorithm in place of the Viterbi. Unfortunately, the option in vcftools is very experimental at the moment, and isn't really ready for "prime time" (hence being labelled under "Options still in development"). Specifically, the option is very slow to run on any dataset of reasonable size, and I therefore don't recommend the option for regular use.
Regards, Adam
Thanks Adam. I have tested the LROH option on some non-human data and got some interesting results that I want to investigate further. Is there any reason to believe that running the LROH option would be problematic for mouse or rat genomes, for instance if it incorporates assumptions about recombination rate based on a human reference? Just want to check because it's not clear exactly how VCFTools implements the Auton et al., algorithm. Best, Rubal
If I have interpreted the Auton et al. 2009 paper correctly, the algorithm will find ROH at least 1cM in length that have at least 50 SNPs. Is the number of SNPs cumulative across individuals, such that 50 individuals could have a single (different) SNP in this region? This is the only solution that comes to mind to explain my output file, which looks like this (truncated, of course):
CHROM AUTO_START AUTO_END N_VARIANTS INDV
chr6 3192774 7941907 85 M103
chr6 32714130 32714172 1 M103
chr6 32965687 33317372 9 M103
chr6 35146229 35975515 54 M103
chr6 18166887 18166904 8 M105r
chr6 18166908 18526735 19 M105
chr6 20216335 20216336 1 M113 ## this line with the small interval
chr6 20216340 20216341 1 M113
chr6 20216343 20216345 1 M113
chr6 20216350 20216356 1 M113
It's not clear to me why some of the regions (e.g., the line with the comment) are so small.
Thanks,
Loren
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sackettl •
The option in VCFtools just outputs all regions where the probability of autozygosity is about 0.99. It is left to the user to filter these events as required.
I've actually made a few changes to the LROH option in the past couple of days, so the function should be a little more informative (and run slightly more efficiently). These changes are now available in the SVN version.
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Hi,
I'm running this command:
and getting this log on the screen:
But the output file contains only the header. Even if I do
--stdoutI also get the header only.I don't know what's the problem.
Thanks!
Hi,
I am having the same problem. After running the
-LROHcommand I get only the header line in output file. Can someone please explain on this.Thank you
Best
Rangi
Hello! I too am running into the same issue! Can anyone explain this?!!
Thank you!
It might be helpful depending on your chromosome names to include quotes around them as in, --chr "chromname". I hope that helps!