how can i get filtered position?

[ruizgo]

I use command python /opt/hap.py/bin/hap.py trust.vcf test.vcf.gz -T /data/target.bed -o ./test In summary file，filter column，I can see ALL,PASS，But i didn't find the location filtered, how to find it?thks

[b-math]

Hello.

By appending the -V flag to the command, you get a combined vcf, where each position in query and truth is listed and whether it is found.

Hope, that answers your question. Best regards