The example command in the document of PB3.7 cannot be excuted normally. I change the --mapq to --map-quality as shown in the help.
pbrun vcfqc \
--in-vcf HG002.hiseqx.pcr-free.30x.pb.deepvariant.vcf \
--output-dir HG002.hiseqx.pcr-free.30x.pb.deepvariant.qc \
--map-quality MAPQ \
--depth DP \
--allele-depth AD \
--vaf AF
There are many warnings as:
[PB Warning 2022-May-26 01:02:10][src/report.cpp:217] Warning: Depth values being assumed as ints even though they are not: DP
[PB Warning 2022-May-26 01:02:10][src/report.cpp:208] Warning: allele depth values being assumed as ints even though they are not: AD