hudsonalpha / csl_public_benchmark Goto Github PK

We've had some questions about the reference origins. We should probably add some links to file and bash scripts where applicable with regards to reference acquisition.

Hi,
Thanks for testing dysgu, I have a few questions about whats causing the low precision values of dysgu. Firstly, I just wanted to compare notes about how you test using truvari. I have tested with:
grep '#\|PASS' HG002.dysgu.vcf | grep '#\|DEL' > HG002.dysgu_pass.del.vcf; bgzip HG002.dysgu_pass.del.vcf; tabix HG002.dysgu_pass.del.vcf; truvari bench -b HG002_SVs_Tier1_v0.6.vcf.gz --includebed HG002_SVs_Tier1_v0.6_include.bed --sizemax 260000000 --giabreport -c HG002.dysgu_pass.del.vcf.gz -o truvari_dysgu_pass_only_del --pctsim 0 -s 50 --passonly
Also was interested to know what coverage and read length your samples are.
Finally I noticed in the dysgu results the stdev of the precision values seemed very high, for example on the hg38 GIAB masked dragmap-1.2.1 precision score was 0.4321+-0.2749. Im not sure whats causing this, but possibly the insert size metrics are not being worked out properly? This should be available in the log file from dysgu. Thanks!