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Graphtyper flag may need to be added if working with Nanopore data otherwise empty merged vcf file #70
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I just checked and reproduced this behavior in the pipeline. Without |
That is a good question and something I wondered too. I'm looking into what happens when I call variants with and without the flag, for a small dataset of short read samples. |
I did a fast experiment. I had 6 short read p. ramorum samples and I ran graphtyper exactly the same, except for the added flag or not. I then only filtered SNPs as the pipeline does. When I look at pairwise SNP differences between samples, results are very similar, but not identical. It seems for each sample pair, there are between 15-30 more SNP differences identified in the graphtyper analysis where the flag is used. |
Nice! Those look very similar. If that is representative of most datasets then I think we can just leave this flag always on for now. |
Description of the bug
In discussion with Alex, Upasana, and Fernanda, we realized that we likely need to include the flag
--no_filter_on_proper_pairs
when using thegraphtyper genotype
command with the 150-bp trimmed long reads.(Thanks to Alex for bringing to our attention these additional parameters under
graphtyper genotype --advanced --help
).If you don't use this, we found that if you merge your individual vcf files, using
graphtyper vcf_concatenate
command, the final merged output file is empty and no variants are called.Command used and terminal output
No response
Relevant files
No response
System information
No response
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