The example command in the document of PB3.7 cannot be excuted normally. I change the
--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