Picard vcf filtering
Hi, I use Picard to filter a vcf file. It seems not to function propely. I am filtering on read depth using MIN_DP=50 but I still see a lot of genotypes in the resulting file with lower coverage than 50.
Here is my call:
java -jar /tools/picard-2.9.0/picard.jar FilterVcf I=output.vcf O=output2.vcf MIN_AB=0.4 MIN_DP=50 MIN_GQ=30