invalid vcf output (according to Picard)

[parlar]

Hi, I'm working on integrating lofreq into the bcbio-nextgen framework/pipeline but ran into an issue.

Bcbio uses gathervcfs (Picard) but does not work since chromsomes/contigs are missing from the lofreq output vcf header. This can be corrected using the Picard UpdateVcfSequenceDictionary tool but it cannot be piped, unfortunately. If possible, I'd rather avoid using temp files or some homegrown script to solve the issue.

Would it be possible to update lofreq to make it produce vcfs that are accepted by Picard?

[andreas-wilm]

Hi Pär, apologies for the late reply. Could you share an example of missing chromosomes/contigs? I don't see this mentioned in the vcf specification. It would be ideal if you could share files and commands to reproduce this. Many thanks, Andreas

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On Wed, 2 Sep 2020 at 20:02, Pär Larsson ***@***.***> wrote: Hi, I'm working on integrating lofreq into the bcbio-nextgen framework/pipeline but ran into an issue. Bcbio uses gathervcfs (Picard) but does not work since chromsomes/contigs are missing from the lofreq output vcf header. This can be corrected using the Picard UpdateVcfSequenceDictionary tool but cannot be piped, unfortunately. If possible, I'd rather avoid using temp files or some homegrown script to solve the issue. Would it be possible to update lofreq to make it produce vcfs that are accepted by Picard? — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#101>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAILSCNBFY7UNOMEV5K6D2TSDYX4PANCNFSM4QS5PJSA> .

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