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> 30,000 variants reported from trio-analysis with FPR 0.001? #386
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Hi @moldach. How many of those calls have a Given the amount of memory you're using for each sample, I'm wondering what your coverage is. I tested mostly trios with 30x-50x average coverage. You're using much more memory than I ever did, and if that is due to high coverage you might need to fiddle with the case/control abundance thresholds a bit as well. I hope this helps! |
Didn't think of that! I think two of the I tried using
|
I can't say that I'm familiar with $ # Just count the variants passing filters
$ grep -c $'\tPASS\t' calls.scored.sorted.vcf
$
$ # Actually retrieve the passing variants
$ grep $'\tPASS\t' calls.scored.sorted.vcf > output.vcf |
Okay thank you. But, riddle me this,
|
Most likely explanation: while the lower FPR offers better theoretical accuracy, both FPRs offer identical effective accuracy. A more thorough investigation of the 3k PASSing variants may reveal another more interesting story though. |
To be clear, I meant another additional story, not another alternative story. |
I'm seeing a very high number of reported variants from
kevlar
.Even after restricting the
max_fpr
values to0.001
I'm seeing> 30,000
variants?config.json
Counting lines in output
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