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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.