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tgen / vcfMerger2

Dynamic vcfMerger for 2 to N somatic variants vcf files
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Octopus AD value are single number separated by commas. #17

Closed ChristopheLegendre closed 4 years ago

ChristopheLegendre commented 4 years ago

0|1:61:0:6,8,6,8 0|0:65:0.12:7,7,8,8 is the issue; should be: 0|1:61:0:68,68 0|0:65:0.12:77,88

ChristopheLegendre commented 4 years ago

That one was tricky. Despite adding the new AD field to the vcf Header and processing the AD the same way for ALL the tools, Octopus outputted the AD as a string and not an integer despite the definition of AD as Integer in vcfMerger2.

It happens that the header was not updated correctly because AD was already present in the original Octopus' VCF and therefore the update in vcfMerger2 does not take place using the update_header function of cyvcf2; Not Only the AD was present and not updated according to the specs defined by vcfMerger2 (which was correct by the way), but the definition of AD in the original Octopus' vcf was wrong; AD was defined as a string instead of integer and that is what created the issue in the first place.