I am a newbie using Annovar and just encountered this. I have annotated a vcf file, following the instructions. I have noticed that CADD_phred has dots for some variants and numbers for others.
CADD_phred=.
CADD_phred=0.047
I think this is OK, as I have seen that in some blogs. Can you confirm this?
Now I am trying to filter by CADD>20 using this command using bcftools/1.11:
bcftools view -i "INFO/CADD_phred>20" -Oz -o out.vcf.gz in.vcf.gz
This is the error message:
Error: cannot use arithmetic operators to compare strings and numbers
I have tried to change the header for CADD_phred from string to float and invoked the above command, but it didn't work.
INFO=
INFO=
I am also trying to filter variants by nonsynonymous_SNV and stopgain but I haven't been successful.
Hi,
I am a newbie using Annovar and just encountered this. I have annotated a vcf file, following the instructions. I have noticed that CADD_phred has dots for some variants and numbers for others. CADD_phred=. CADD_phred=0.047 I think this is OK, as I have seen that in some blogs. Can you confirm this? Now I am trying to filter by CADD>20 using this command using bcftools/1.11: bcftools view -i "INFO/CADD_phred>20" -Oz -o out.vcf.gz in.vcf.gz This is the error message: Error: cannot use arithmetic operators to compare strings and numbers
I have tried to change the header for CADD_phred from string to float and invoked the above command, but it didn't work.
INFO=
INFO=
I am also trying to filter variants by nonsynonymous_SNV and stopgain but I haven't been successful.
Any idea how to proceed? Thanks in advance