Describe the bug
The version of bcftools is 1.9, while the latest version of the time I am writing is 1.20, and between the two versions, there exist different behaviors when handling vcf data with --filter-regions or -R options. It was reported in the official repository on the following links: https://github.com/samtools/bcftools/issues/221, https://github.com/samtools/bcftools/issues/1374, and they are fixed since 1.12 version.
Expected behavior
The following command should work
Input data
vcffile: wgs.vcf.gz
bedfile: s3://aim-data-dependencies-2.0/filter_exonic/hg19.bed
Screenshots or pipeline output
Additional context
Even though the current version is not using the parameter, I was about to use the parameter to implement exonic filter on the pipeline, and found out it was not working on the docker while it worked on my machine, which had higher version of bcftools.
jylee-bcm
commented
3 months ago
Describe the bug The version of bcftools is 1.9, while the latest version of the time I am writing is 1.20, and between the two versions, there exist different behaviors when handling vcf data with
--filter-regionsor-Roptions. It was reported in the official repository on the following links: https://github.com/samtools/bcftools/issues/221, https://github.com/samtools/bcftools/issues/1374, and they are fixed since 1.12 version.Expected behavior The following command should work
Input data vcffile: wgs.vcf.gz bedfile:
s3://aim-data-dependencies-2.0/filter_exonic/hg19.bedScreenshots or pipeline output
Additional context Even though the current version is not using the parameter, I was about to use the parameter to implement exonic filter on the pipeline, and found out it was not working on the docker while it worked on my machine, which had higher version of bcftools.