Michael Yourshaw

make fails with htslib 1.13 (1.11 OK)

1

`cmake -DHTS_INCLUDE_DIRS=${INSTALL_DIR}/include/ -DHTS_LIBRARIES=${INSTALL_DIR}/lib/libhts.a .. -- The C compiler identification is GNU 10.3.0 -- The CXX compiler identification is GNU 10.3.0 -- Detecting C compiler ABI info -- Detecting C compiler...

FILTER line is malformed

2

Background: In FILTER, multiple filters should be separated by semicolons. The widely used, but not actively maintained, VarScan2 genomic variant caller uses commas instead. Moreover, VarScan2 does not add ##FILTER...

install fails if setuptools >= 58

1

pip3 install PyVCF (version 0.6.8) will fail when setuptools version is >=58. Instead PyVCF will install version 0.4.3, which fails to run with this error: ImportError: cannot import name 'Reader'...

In a VCF file created by the GATK pipeline, there can be various statistics in the INFO field that have a value of `nul`. See the attached example VCF. For...

Id list

1

from the VCF spec: "ID - identifier: **Semi-colon separated list** of unique identifiers where available. If this is a dbSNP variant it is encouraged to use the rs number(s). No...