Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
How to merge the sample_X_genotyped_intervals.vcf files created by PostprocessGermlineCNVCalls?
How to merge the sample_X_genotyped_intervals.vcf files created by PostprocessGermlineCNVCalls to a multi-sample VCF file?
The files all have the same bins/records, so it should be easy to created a multi-sample VCF of these files.
I normally use bcftools to merge vcf files. bcftools merge gives the following error when trying to merge the (bgzipped, tabix indexed) sample_X_genotyped_intervals.vcf files created by PostprocessGermlineCNVCalls
Incorrect number of FORMAT/CNLP values at Chr_01:1001, cannot merge. The tag is defined as Number=A, but found 6 values and 3 alleles. See also http://samtools.github.io/bcftools/howtos/FAQ.html#incorrect-nfields
Can you check if the FORMAT declaration of CNLP is correct.
And advise on if there is a tool in GATK to merge single sample vcf files (created by PostprocessGermlineCNVCalls) to a multi-sample VCF file.
For time being I wrote my own python text parsing script to create the multi-sample VCF file.
But this seems like something that should be possible with GATK or bcftools.