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GS working on melanogaster but...
I've managed to get my deletion caller to generate a genotypes.vcf with complete calls, running on 20 flies, covering 2 million bases, search for events between 100bp and 10,000 bp. This detects 104 deletions although only 2 pass the quality control. Most of the other variants have 'low depth' although many are high population frequency. I'm not sure whether to keep these in or not. If I do 200 individuals at 160 million bases will this alter the default thresholds and improve the pass rate?
I'm running the script on a Sun Grid Engine active login with
-pe openmp 30
for the whole job, and
-jobNative '-V -pe openmp 10 -q bioinf.q' \
within each command, which took two days to complete.
Also I was wondering how easy it is to extract the call metrics from the vcf, and whether custom thresholds are advised. Does anyone use vcftools, GATK vcfToTable, or do we need to write a custom script?
Any tips would be handy. Cheers,